Mercurial > repos > elixir-it > fpfilter
changeset 0:276875076be1 draft
Uploaded
| author | elixir-it |
|---|---|
| date | Tue, 03 Jul 2018 06:05:44 -0400 |
| parents | |
| children | 0f17ca98338e |
| files | fpfilter.pl fpfilter.xml test-data/input_vcf.vcf test-data/output_vcf.vcf |
| diffstat | 4 files changed, 6331 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fpfilter.pl Tue Jul 03 06:05:44 2018 -0400 @@ -0,0 +1,596 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Getopt::Long; +use IO::File; +use File::Temp qw( tempdir ); +use File::Spec; +use Cwd qw( abs_path cwd); + +## Define filtering parameters ## + +my $min_read_pos = 0.10; +my $max_read_pos = 1 - $min_read_pos; +my $min_var_freq = 0.05; +my $min_var_count = 4; + +my $min_strandedness = 0.01; +my $max_strandedness = 1 - $min_strandedness; + +my $max_mm_qualsum_diff = 50; +my $max_mapqual_diff = 30; +my $max_readlen_diff = 25; +my $min_var_dist_3 = 0.20; +my $max_var_mm_qualsum = 100; + + +## Parse arguments ## + +my $output_basename; + +my $vcf_file; +my $output_file; +my $bam_file; +my $bam_index; +my $sample; +my $bam_readcount_path = 'bam-readcount'; +my $samtools_path = 'samtools'; +my $ref_fasta; +my $help; + + +my $opt_result; +my @params = @ARGV; + +$opt_result = GetOptions( + 'vcf-file=s' => \$vcf_file, + 'bam-file=s' => \$bam_file, + 'bam-index=s' => \$bam_index, + 'sample=s' => \$sample, + 'bam-readcount=s' => \$bam_readcount_path, + 'samtools=s' => \$samtools_path, + 'reference=s' => \$ref_fasta, + 'output=s' => \$output_file, + 'min-read-pos=f' => \$min_read_pos, + 'min-var-freq=f' => \$min_var_freq, + 'min-var-count=f' => \$min_var_count, + 'min-strandedness=f' => \$min_strandedness, + 'max-mm-qualsum-diff=f' => \$max_mm_qualsum_diff, + 'max-mapqual-diff=f' => \$max_mapqual_diff, + 'max-readlen-diff=f' => \$max_readlen_diff, + 'min-var-dist-3=f' => \$min_var_dist_3, + 'max-var-mm-qualsum=f' => \$max_var_mm_qualsum, + 'help' => \$help, +); + +unless($opt_result) { + die help_text(); +} + +if($help) { + print STDOUT help_text(); + exit 0; +} + +unless($vcf_file) { + warn "You must provide a file to be filtered\n"; + die help_text(); +} + +unless(-s $vcf_file) { + die "Can not find VCF file: $vcf_file\n"; +} + +unless($ref_fasta) { + warn "You must provide a reference fasta for generating readcounts to use for filtering\n"; + die help_text(); +} + +unless(-s $ref_fasta) { + die "Can not find valid reference fasta: $ref_fasta\n"; +} + +unless($bam_file) { + die "You must provide a BAM file for generating readcounts\n"; + die help_text(); +} + +unless(-s $bam_file) { + die "Can not find valid BAM file: $bam_file\n"; +} + +if($bam_index && !-s $bam_index) { + die "Can not find valid BAM index file: $bam_index\n"; +} + +unless($output_file) { + warn "You must provide an output file name: $output_file\n"; + die help_text(); +} +else { + $output_file = abs_path($output_file); #make sure we have full path as manipulating cwd below +} + +unless($sample) { + warn "You must provide a sample name\n"; + die help_text(); +} + +my %filters; +$filters{'position'} = [sprintf("PB%0.f",$min_read_pos*100), "Average position on read less than " . $min_read_pos . " or greater than " . $max_read_pos . " fraction of the read length"]; +$filters{'strand_bias'} = [sprintf("SB%0.f",$min_strandedness*100), "Reads supporting the variant have less than " . $min_strandedness . " fraction of the reads on one strand, but reference supporting reads are not similarly biased"]; +$filters{'min_var_count'} = [ "MVC".$min_var_count, "Less than " . $min_var_count . " high quality reads support the variant"]; +$filters{'min_var_freq'} = [ sprintf("MVF%0.f",$min_var_freq*100), "Variant allele frequency is less than " . $min_var_freq]; +$filters{'mmqs_diff'} = [ sprintf("MMQSD%d",$max_mm_qualsum_diff), "Difference in average mismatch quality sum between variant and reference supporting reads is greater than " . $max_mm_qualsum_diff]; +$filters{'mq_diff'} = [ sprintf("MQD%d",$max_mapqual_diff), "Difference in average mapping quality sum between variant and reference supporting reads is greater than " . $max_mapqual_diff]; +$filters{'read_length'} = [ sprintf("RLD%d",$max_readlen_diff), "Difference in average clipped read length between variant and reference supporting reads is greater than " . $max_readlen_diff]; +$filters{'dist3'} = [ sprintf("DETP%0.f",$min_var_dist_3*100), "Average distance of the variant base to the effective 3' end is less than " . $min_var_dist_3]; +$filters{'var_mmqs'} = [ sprintf("MMQS%d",$max_var_mm_qualsum), "The average mismatch quality sum of reads supporting the variant is greater than " . $max_var_mm_qualsum] if($max_var_mm_qualsum); +$filters{'no_var_readcount'} = [ "NRC", "Unable to grab readcounts for variant allele"]; +$filters{'incomplete_readcount'} = [ "IRC", "Unable to grab any sort of readcount for either the reference or the variant allele"]; + +my $vcf_header; +my @vcf_lines; + +my %rc_for_snp; # store info on snp positions and VCF line +my %rc_for_indel; #store info on indel positions and VCF line + +my ($workdir, $working_fasta, $working_bam) = setup_workdir($ref_fasta, $bam_file, $bam_index); + +my $starting_dir = cwd(); + +my $input = IO::File->new($vcf_file) or die "Unable to open input file $vcf_file: $!\n"; +$vcf_header = parse_vcf_header($input); +add_filters_to_vcf_header($vcf_header, values %filters); +add_process_log_to_header($vcf_header, $vcf_file, @params); + +my $header_line = $vcf_header->[-1]; +chomp $header_line; +my @header_fields = split "\t", $header_line; + +while(my $entry = $input->getline) { + push @vcf_lines, $entry; + chomp $entry; + + my %fields; + @fields{@header_fields} = split("\t", $entry); + + my $filter_sample = $fields{$sample}; + unless($filter_sample) { + die "Unable to find field for $sample\n"; + } + my @sample_fields = split /:/, $filter_sample; + unless(@sample_fields) { + die "Unable to parse field for $sample\n"; + } + my $index = 0; + my %format_keys = map { $_ => $sample_fields[$index++] } split /:/, $fields{FORMAT}; + #these are in order ACGT + my @alleles = ($fields{REF}, split /,/, $fields{ALT}); + my %gt_alleles = map {$_ => 1} grep { $_ > 0 } split /\//, $format_keys{GT}; + my @used_alleles; + for my $allele_index (keys %gt_alleles) { + push @used_alleles, $alleles[$allele_index]; + } + my ($var) = sort @used_alleles; #follow existing convention of fp filter using alphabetical order to choose a single base on triallelic sites + $var = q{} unless defined $var; #in the case where there is no variant allele, set this to the empty string. Later it will be filtered as NRC or IRC + $var = uc($var); + my $ref = uc($fields{REF}); + my $chrom = $fields{'#CHROM'}; + my $pos = $fields{POS}; + + if(length($ref) > 1 || length($var) > 1) { + #it's an indel or mnp + if(length($ref) == length($var)) { + die "MNPs unsupported\n"; + } + elsif(length($ref) > length($var)) { + #it's a deletion + $pos += 1; + ($ref, $var) = ($var, $ref); + $ref = substr($var, 1, 1); + $var = "-" . substr($var, 1); + } + else { + #it's an insertion + substr($var, 0, 1, "+"); + } + $rc_for_indel{$chrom}{$pos}{$ref}{$var} = \$vcf_lines[-1]; + } + else { + #it's a SNP + $rc_for_snp{$chrom}{$pos}{$ref}{$var} = \$vcf_lines[-1]; + } +} + +if(%rc_for_snp) { + filter_sites_in_hash(\%rc_for_snp, $bam_readcount_path, $working_bam, $working_fasta, $workdir); +} +else { + print STDERR "No SNP sites identified\n"; +} + +if(%rc_for_indel) { + filter_sites_in_hash(\%rc_for_indel, $bam_readcount_path, $working_bam, $working_fasta, $workdir, '-i'); +} +else { + print STDERR "No Indel sites identified\n"; +} + +## Open the output files ## +my $filtered_vcf = IO::File->new("$output_file","w") or die "Can't open output file $output_file: $!\n"; +print $filtered_vcf @$vcf_header; +print $filtered_vcf @vcf_lines; + +chdir $starting_dir or die "Unable to go back to starting dir\n"; +exit(0); + +################################################################################ + +=head3 read_counts_by_allele + + Retrieve relevant read counts for a certain allele + + +=cut + +sub read_counts_by_allele { + (my $line, my $allele) = @_; + + my @lineContents = split(/\t/, $line); + my $numContents = @lineContents; + + for(my $colCounter = 5; $colCounter < $numContents; $colCounter++) { + my $this_allele = $lineContents[$colCounter]; + my @alleleContents = split(/\:/, $this_allele); + if($alleleContents[0] eq $allele) { + my $numAlleleContents = @alleleContents; + + return("") if($numAlleleContents < 8); + + my $return_string = ""; + my $return_sum = 0; + for(my $printCounter = 1; $printCounter < $numAlleleContents; $printCounter++) { + $return_sum += $alleleContents[$printCounter]; + $return_string .= "\t" if($return_string); + $return_string .= $alleleContents[$printCounter]; + } + + return($return_string); + + } + } + + return(""); +} + + +sub help_text { + return <<HELP; +fpfilter - Filtering for Illumina Sequencing + +SYNOPSIS +fpfilter [options] [file ...] + +OPTIONS +--vcf-file the input VCF file. Must have a GT field. +--bam-file the BAM file of the sample you are filtering on. Typically the tumor. +--sample the sample name of the sample you want to filter on in the VCF file. +--reference a fasta containing the reference sequence the BAM file was aligned to. +--output the filename of the output VCF file +--min-read-pos minimum average relative distance from start/end of read +--min-var-freq minimum variant allele frequency +--min-var-count minimum number of variant-supporting reads +--min-strandedness minimum representation of variant allele on each strand +--max-mm-qualsum-diff maximum difference of mismatch quality sum between variant and reference reads (paralog filter) +--max_var_mm_qualsum maximum mismatch quality sum of reference-supporting reads +--max-mapqual-diff maximum difference of mapping quality between variant and reference reads +--max-readlen-diff maximum difference of average supporting read length between variant and reference reads (paralog filter) +--min-var-dist-3 minimum average distance to effective 3prime end of read (real end or Q2) for variant-supporting reads +--help this message + +DESCRIPTION +This program will filter a VCF with a variety of filters as detailed in the VarScan2 paper (http://www.ncbi.nlm.nih.gov/pubmed/22300766). It requires the bam-readcount utility (https://github.com/genome/bam-readcount). + +This filter was calibrated on 100bp PE Illumina reads. It is likely to be overly stringent for longer reads and may be less effective on shorter reads. + +AUTHORS +Dan Koboldt Original code +Dave Larson Modifications for VCF and exportation. + +HELP +} + +### methods copied from elsewhere begin here... +sub parse_vcf_header { + my $input_fh = shift; + + my @header; + my $header_end = 0; + while (!$header_end) { + my $line = $input_fh->getline; + if ($line =~ m/^##/) { + push @header, $line; + } elsif ($line =~ m/^#/) { + push @header, $line; + $header_end = 1; + } else { + die "Missed the final header line with the sample list? Last line examined: $line Header so far: " . join("\n", @header) . "\n"; + } + } + return \@header; +} + +sub generate_region_list { + my ($hash, $region_fh) = @_; #input_fh should be a filehandle to the VCF + print STDERR "Printing variants to temporary region_list file...\n"; + for my $chr (keys %$hash) { + for my $pos (sort { $a <=> $b } keys %{$hash->{$chr}}) { + print $region_fh "$chr\t$pos\t$pos\n"; + } + } +} + +sub _simplify_indel_allele { + my ($ref, $var) = @_; + #these could be padded e.g. G, GT for a T insertion or GCC G for a 2bp deletion + #they could also be complex e.g. GCCCGT, GCGT for a 2bp deletion + #they could also represent an insertion deletion event e.g. GCCCGT GCGGGGT; these cannot be represented in genome bed. Throw an error or warn. + # + #I think the algorithm should be trim end (no updating of coords required) + #trim beginning and return number of bases trimmed + + my @ref_array = map { uc } split //, $ref; + my @var_array = map { uc } split //, $var; + + while(@ref_array and @var_array and $ref_array[-1] eq $var_array[-1]) { + pop @ref_array; + pop @var_array; + } + + my $right_shift = 0; + while(@ref_array and @var_array and $ref_array[0] eq $var_array[0]) { + shift @ref_array; + shift @var_array; + $right_shift++; + } + + return (join("",@ref_array), join("",@var_array), $right_shift); +} + +sub filter_site { + my ($ref_result, $var_result) = @_; + #this will return a list of filter names + my @filter_names; + if($ref_result && $var_result) { + ## Parse out the bam-readcounts details for each allele. The fields should be: ## + #num_reads : avg_mapqual : avg_basequal : avg_semq : reads_plus : reads_minus : avg_clip_read_pos : avg_mmqs : reads_q2 : avg_dist_to_q2 : avgRLclipped : avg_eff_3'_dist + my ($ref_count, $ref_map_qual, $ref_base_qual, $ref_semq, $ref_plus, $ref_minus, $ref_pos, $ref_subs, $ref_mmqs, $ref_q2_reads, $ref_q2_dist, $ref_avg_rl, $ref_dist_3) = split(/\t/, $ref_result); + my ($var_count, $var_map_qual, $var_base_qual, $var_semq, $var_plus, $var_minus, $var_pos, $var_subs, $var_mmqs, $var_q2_reads, $var_q2_dist, $var_avg_rl, $var_dist_3) = split(/\t/, $var_result); + + my $ref_strandedness = my $var_strandedness = 0.50; + $ref_dist_3 = 0.5 if(!$ref_dist_3); + + ## Use conservative defaults if we can't get mismatch quality sums ## + $ref_mmqs = 50 if(!$ref_mmqs); + $var_mmqs = 0 if(!$var_mmqs); + my $mismatch_qualsum_diff = $var_mmqs - $ref_mmqs; + + ## Determine map qual diff ## + + my $mapqual_diff = $ref_map_qual - $var_map_qual; + + + ## Determine difference in average supporting read length ## + + my $readlen_diff = $ref_avg_rl - $var_avg_rl; + + + ## Determine ref strandedness ## + + if(($ref_plus + $ref_minus) > 0) { + $ref_strandedness = $ref_plus / ($ref_plus + $ref_minus); + $ref_strandedness = sprintf("%.2f", $ref_strandedness); + } + + ## Determine var strandedness ## + + if(($var_plus + $var_minus) > 0) { + $var_strandedness = $var_plus / ($var_plus + $var_minus); + $var_strandedness = sprintf("%.2f", $var_strandedness); + } + + if($var_count && ($var_plus + $var_minus)) { + ## We must obtain variant read counts to proceed ## + + my $var_freq = $var_count / ($ref_count + $var_count); + + ## FAILURE 1: READ POSITION ## + if(($var_pos < $min_read_pos) || ($var_pos > $max_read_pos)) { + #$stats{'num_fail_pos'}++; + push @filter_names, $filters{'position'}->[0]; + } + + ## FAILURE 2: Variant is strand-specific but reference is NOT strand-specific ## + if(($var_strandedness < $min_strandedness || $var_strandedness > $max_strandedness) && ($ref_strandedness >= $min_strandedness && $ref_strandedness <= $max_strandedness)) { + #$stats{'num_fail_strand'}++; + push @filter_names, $filters{'strand_bias'}->[0]; + } + + ## FAILURE : Variant allele count does not meet minimum ## + if($var_count < $min_var_count) { + #$stats{'num_fail_varcount'}++; + push @filter_names, $filters{'min_var_count'}->[0]; + } + + ## FAILURE : Variant allele frequency does not meet minimum ## + if($var_freq < $min_var_freq) { + #$stats{'num_fail_varfreq'}++; + push @filter_names, $filters{'min_var_freq'}->[0]; + } + + ## FAILURE 3: Paralog filter for sites where variant allele mismatch-quality-sum is significantly higher than reference allele mmqs + if($mismatch_qualsum_diff> $max_mm_qualsum_diff) { + #$stats{'num_fail_mmqs'}++; + push @filter_names, $filters{'mmqs_diff'}->[0]; + } + + ## FAILURE 4: Mapping quality difference exceeds allowable maximum ## + if($mapqual_diff > $max_mapqual_diff) { + #$stats{'num_fail_mapqual'}++; + push @filter_names, $filters{'mq_diff'}->[0]; + } + + ## FAILURE 5: Read length difference exceeds allowable maximum ## + if($readlen_diff > $max_readlen_diff) { + #$stats{'num_fail_readlen'}++; + push @filter_names, $filters{'read_length'}->[0]; + } + + ## FAILURE 5: Read length difference exceeds allowable maximum ## + if($var_dist_3 < $min_var_dist_3) { + #$stats{'num_fail_dist3'}++; + push @filter_names, $filters{'dist3'}->[0]; + } + + if($max_var_mm_qualsum && $var_mmqs > $max_var_mm_qualsum) { + #$stats{'num_fail_var_mmqs'}++; + push @filter_names, $filters{'var_mmqs'}->[0]; + } + + ## SUCCESS: Pass Filter ## + if(@filter_names == 0) { + #$stats{'num_pass_filter'}++; + ## Print output, and append strandedness information ## + @filter_names = ('PASS'); + } + + } + else { + push @filter_names, $filters{'no_var_readcount'}->[0]; + } + } + else { + #$stats{'num_no_readcounts'}++; + #print $fail_fh "$line\tno_readcounts\n"; + push @filter_names, $filters{'incomplete_readcount'}->[0]; + } + return @filter_names; +} + +sub add_filters_to_vcf_header { + my ($parsed_header, @filter_refs) = @_; + my $column_header = pop @$parsed_header; + for my $filter_ref (@filter_refs) { + my ($filter_name, $filter_description) = @$filter_ref; + my $filter_line = qq{##FILTER=<ID=$filter_name,Description="$filter_description">\n}; + push @$parsed_header, $filter_line; + } + push @$parsed_header, $column_header; +} + +sub add_process_log_to_header { + my ($parsed_header, $input, @params) = @_; + my $column_header = pop @$parsed_header; + my $param_string = join(" ", @params); + push @$parsed_header, qq{##vcfProcessLog=<InputVCF=<$input>, InputVCFSource=<fpfilter>, InputVCFVer=<6.0>, InputVCFParam=<"$param_string"> InputVCFgeneAnno=<.>>\n}, $column_header; +} + +sub filter_sites_in_hash { + my ($hash, $bam_readcount_path, $bam_file, $ref_fasta, $working_dir, $optional_param) = @_; + #done parsing vcf + $optional_param ||= ''; + my $list_name = File::Spec->catfile($working_dir, "regions.txt"); + my $list_fh = IO::File->new($list_name,"w") or die "Unable to open file for coordinates\n"; + generate_region_list($hash, $list_fh); + $list_fh->close(); + +## run bam-readcount + my $bam_readcount_cmd = "$bam_readcount_path -f $ref_fasta -l $list_name -w 0 -b 20 $optional_param $bam_file|"; + my $rc_results = IO::File->new($bam_readcount_cmd) or die "Unable to open pipe to bam-readcount cmd: $bam_readcount_cmd\n"; + while(my $rc_line = $rc_results->getline) { + chomp $rc_line; + my ($chrom, $position) = split(/\t/, $rc_line); + if($hash->{$chrom}{$position}) { + for my $ref (keys %{$hash->{$chrom}{$position}}) { + for my $var (keys %{$hash->{$chrom}{$position}{$ref}}) { + my $ref_result = read_counts_by_allele($rc_line, $ref); + my $var_result = read_counts_by_allele($rc_line, $var); + my @filters = filter_site($ref_result, $var_result); + + my $vcf_line_ref = $hash->{$chrom}{$position}{$ref}{$var}; + my @fields = split "\t", $$vcf_line_ref; + if($fields[6] eq '.' || $fields[6] eq 'PASS') { + $fields[6] = join(";", @filters); + } + else { + $fields[6] = join(";", $fields[6], @filters) if($filters[0] ne 'PASS'); + } + $$vcf_line_ref = join("\t", @fields); + } + } + } + else { + die "Unknown site for rc\n"; + } + } + unless($rc_results->close) { + die "Error running bam-readcount\n"; + } +} + +sub setup_workdir { + my ($reference, $bam_file, $bam_index) = @_; + $reference = abs_path($reference); + $bam_file = abs_path($bam_file); + $bam_index = abs_path($bam_index) if $bam_index; + + my $dir = File::Temp->newdir('fpfilterXXXXX', TMPDIR => 1, CLEANUP => 1, DIR => './') or + die "Unable to create working directory\n"; + + #symlink in necessary files to run + my $working_reference = File::Spec->catfile($dir, "reference.fa"); + symlink $reference, $working_reference; + + my $fa_index = $reference . ".fai"; + unless(-e $fa_index) { + index_fasta($working_reference); + } + else { + symlink $fa_index, File::Spec->catfile($dir, "reference.fa.fai"); + } + + my $working_bam = File::Spec->catfile($dir, "tumor.bam"); + my $working_bam_index = File::Spec->catfile($dir, "tumor.bam.bai"); + symlink $bam_file, $working_bam; + if($bam_index) { + symlink $bam_index, $working_bam_index; + } + elsif(-e $bam_file . ".bai") { + symlink $bam_file . ".bai", $working_bam_index; + } + else { + index_bam($working_bam); + } + return ($dir, $working_reference, $working_bam); +} + +sub index_fasta { + my ($fasta) = @_; + + print STDERR "Indexing fasta...\n"; + my @args = ($samtools_path, "faidx", $fasta); + system(@args) == 0 + or die "Unable to index $fasta: $?\n"; +} + +sub index_bam { + my ($bam) = @_; + + print STDERR "Indexing BAM...\n"; + my @args = ($samtools_path, "index", $bam); + system(@args) == 0 + or die "Unable to index $bam: $?\n"; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fpfilter.xml Tue Jul 03 06:05:44 2018 -0400 @@ -0,0 +1,77 @@ +<tool id="fpfilter" name="fpfilter" version="0.0.1"> + <description></description> + <requirements> + <requirement type="package" version="0.8" >bam-readcount</requirement> + <requirement type="package" >samtools</requirement> + </requirements> + <command> + perl $__tool_directory__/fpfilter.pl + --vcf-file ${vcf} + --bam-file ${bam} + --bam-index ${bam.metadata.bam_index} + --sample ${sample} + --reference ${reference} + --output ${output} + --min-read-pos ${min_read_pos} + --min-var-freq ${min_var_freq} + --min-var-count ${min_var_count} + --min-strandedness ${min_strandness} + --max-mm-qualsum-diff ${max_mm_qualsum_diff} + --max-var-mm-qualsum ${max_var_mm_qualsum} + --max-mapqual-diff ${max_mapqual_diff} + --max-readlen-diff ${max_readlen_diff} + --min-var-dist-3 ${min_var_dist_3} + </command> + + <inputs> + <param name="vcf" format="vcf" type="data" label="VCF File" help="The input VCF file. Must have a GT field." /> + <param name="bam" format="bam" type="data" label="bam file" help="The BAM file of the sample you are filtering on. Typically the tumor." /> + <param name="sample" type="text" label="Sample" value="sample" help="The sample name of the sample you want to filter on in the VCF file." /> + <param name="reference" format="fasta" type="data" label="Reference Genome" help="A fasta containing the reference sequence the BAM file was aligned to"/> + + <param name="min_read_pos" type="float" value="0.10" label="Min Read Pos" help="Minimum average relative distance from start/end of read." /> + <param name="min_var_freq" type="float" value="0.05" label="Min Var Freq" help="Minimum variant allele frequency." /> + <param name="min_var_count" type="integer" value="4" label="Min Var Count" help="Minimum number of variant-supporting reads." /> + + <param name="min_strandness" type="float" value="0.01" label="Min Strandness" help="Minimum representation of variant allele on each strand." /> + <param name="max_mm_qualsum_diff" type="integer" value="50" label="Max mm qualsum diff" help="Maximum difference of mismatch quality sum between variant and reference reads (paralog filter)." /> + + <param name="max_var_mm_qualsum" type="integer" value="100" label="Max var mm qualsum" help="Maximum mismatch quality sum of reference-supporting reads." /> + <param name="max_mapqual_diff" type="integer" value="30" label="Max mapqual diff" help="Maximum difference of mapping quality between variant and reference reads." /> + + <param name="max_readlen_diff" type="integer" value="25" label="Max readlen diff" help="Maximum difference of average supporting read length between variant and reference reads (paralog filter)" /> + <param name="min_var_dist_3" type="float" value="0.20" label="Min var dist 3 " help="minimum average distance to effective 3prime end of read (real end or Q2) for variant-supporting reads" /> + + </inputs> + + <outputs> + <data format="vcf" name="output" label="FP Filtered VCF" /> + </outputs> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <help> + --vcf-file the input VCF file. Must have a GT field. + --bam-file the BAM file of the sample you are filtering on. Typically the tumor. + --sample the sample name of the sample you want to filter on in the VCF file. + --reference-sequence a fasta containing the reference sequence the BAM file was aligned to. + --output the filename of the output VCF file + --min-read-pos minimum average relative distance from start/end of read + --min-var-freq minimum variant allele frequency + --min-var-count minimum number of variant-supporting reads + --min-strandedness minimum representation of variant allele on each strand + --max-mm-qualsum-diff maximum difference of mismatch quality sum between variant and reference reads (paralog filter) + --max_var_mm_qualsum maximum mismatch quality sum of reference-supporting reads + --max-mapqual-diff maximum difference of mapping quality between variant and reference reads + --max-readlen-diff maximum difference of average supporting read length between variant and reference reads (paralog filter) + --min-var-dist-3 minimum average distance to effective 3prime end of read (real end or Q2) for variant-supporting reads + +this wrapper has been developed from the existing script at https://github.com/ucscCancer/fpfilter-tool/blob/master/fpfilter.xml , only the requirement and part of the command line have been changed in order to make it suitable for CONDA + </help> + + <tests> + <test> + </test> + </tests> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_vcf.vcf Tue Jul 03 06:05:44 2018 -0400 @@ -0,0 +1,2823 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=alt_allele_in_normal,Description="Evidence seen in the normal sample"> +##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor"> +##FILTER=<ID=clustered_read_position,Description="Evidence for somatic variant clusters near the ends of reads"> +##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic"> +##FILTER=<ID=homologous_mapping_event,Description="More than three events were observed in the tumor"> +##FILTER=<ID=multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal"> +##FILTER=<ID=panel_of_normals,Description="Seen in at least 2 samples in the panel of normals"> +##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region"> +##FILTER=<ID=strand_artifact,Description="Evidence for alt allele comes from one read direction only"> +##FILTER=<ID=t_lod_fstar,Description="Tumor does not meet likelihood threshold"> +##FILTER=<ID=triallelic_site,Description="Site filtered because more than two alt alleles pass tumor LOD"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele fraction of the event in the tumor"> +##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the alternate allele"> +##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the alternate allele"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description="Fraction of alt reads indicating OxoG error"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=QSS,Number=A,Type=Integer,Description="Sum of base quality scores for each allele"> +##FORMAT=<ID=REF_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the reference allele"> +##FORMAT=<ID=REF_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the reference allele"> +##GATKCommandLine.MuTect2=<ID=MuTect2,Version=3.8-0-ge9d806836,Date="Wed Apr 11 08:55:44 UTC 2018",Epoch=1523436944508,CommandLineOptions="analysis_type=MuTect2 input_file=[tumor.bam, normal.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[position.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=7 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false cosmic=[] normal_panel=[] dbsnp=(RodBinding name= source=UNBOUND) m2debug=false artifact_detection_mode=false initial_tumor_lod=4.0 initial_normal_lod=0.5 tumor_lod=6.3 normal_lod=2.2 dbsnp_normal_lod=5.5 max_alt_alleles_in_normal_count=1 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=30 strand_artifact_lod=2.0 strand_artifact_power_threshold=0.9 enable_strand_artifact_filter=false enable_clustered_read_position_filter=false pir_median_threshold=10.0 pir_mad_threshold=3.0 debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false debug_read_name=null MQ_filtering_level=20 comp=[] annotation=[DepthPerAlleleBySample, BaseQualitySumPerAlleleBySample, TandemRepeatAnnotator, OxoGReadCounts] excludeAnnotation=[SpanningDeletions] out=/export/galaxy/database/files/001/dataset_1160.dat dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 keepRG=null min_base_quality_score=10 errorCorrectReads=false captureAssemblyFailureBAM=false dontUseSoftClippedBases=false justDetermineActiveRegions=false doNotRunPhysicalPhasing=false maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> +##INFO=<ID=ECNT,Number=1,Type=String,Description="Number of events in this haplotype"> +##INFO=<ID=HCNT,Number=1,Type=String,Description="Number of haplotypes that support this variant"> +##INFO=<ID=MAX_ED,Number=1,Type=Integer,Description="Maximum distance between events in this active region"> +##INFO=<ID=MIN_ED,Number=1,Type=Integer,Description="Minimum distance between events in this active region"> +##INFO=<ID=NLOD,Number=1,Type=String,Description="Normal LOD score"> +##INFO=<ID=PON,Number=1,Type=String,Description="Count from Panel of Normals"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=TLOD,Number=1,Type=String,Description="Tumor LOD score"> +##SAMPLE=<ID=NORMAL,SampleName=normal,File=/export/job_work_dir/000/551/working/normal.bam> +##SAMPLE=<ID=TUMOR,SampleName=tumor,File=/export/job_work_dir/000/551/working/tumor.bam> +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr2,length=242193529> +##contig=<ID=chr3,length=198295559> +##contig=<ID=chr4,length=190214555> +##contig=<ID=chr5,length=181538259> +##contig=<ID=chr6,length=170805979> +##contig=<ID=chr7,length=159345973> +##contig=<ID=chr8,length=145138636> +##contig=<ID=chr9,length=138394717> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr15,length=101991189> +##contig=<ID=chr16,length=90338345> +##contig=<ID=chr17,length=83257441> +##contig=<ID=chr18,length=80373285> +##contig=<ID=chr19,length=58617616> +##contig=<ID=chr20,length=64444167> +##contig=<ID=chr21,length=46709983> +##contig=<ID=chr22,length=50818468> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##contig=<ID=chrM,length=16569> +##contig=<ID=chr1_KI270706v1_random,length=175055> +##contig=<ID=chr1_KI270707v1_random,length=32032> +##contig=<ID=chr1_KI270708v1_random,length=127682> +##contig=<ID=chr1_KI270709v1_random,length=66860> +##contig=<ID=chr1_KI270710v1_random,length=40176> +##contig=<ID=chr1_KI270711v1_random,length=42210> +##contig=<ID=chr1_KI270712v1_random,length=176043> +##contig=<ID=chr1_KI270713v1_random,length=40745> +##contig=<ID=chr1_KI270714v1_random,length=41717> +##contig=<ID=chr2_KI270715v1_random,length=161471> +##contig=<ID=chr2_KI270716v1_random,length=153799> +##contig=<ID=chr3_GL000221v1_random,length=155397> +##contig=<ID=chr4_GL000008v2_random,length=209709> +##contig=<ID=chr5_GL000208v1_random,length=92689> +##contig=<ID=chr9_KI270717v1_random,length=40062> +##contig=<ID=chr9_KI270718v1_random,length=38054> +##contig=<ID=chr9_KI270719v1_random,length=176845> +##contig=<ID=chr9_KI270720v1_random,length=39050> +##contig=<ID=chr11_KI270721v1_random,length=100316> +##contig=<ID=chr14_GL000009v2_random,length=201709> +##contig=<ID=chr14_GL000225v1_random,length=211173> +##contig=<ID=chr14_KI270722v1_random,length=194050> +##contig=<ID=chr14_GL000194v1_random,length=191469> +##contig=<ID=chr14_KI270723v1_random,length=38115> +##contig=<ID=chr14_KI270724v1_random,length=39555> +##contig=<ID=chr14_KI270725v1_random,length=172810> +##contig=<ID=chr14_KI270726v1_random,length=43739> +##contig=<ID=chr15_KI270727v1_random,length=448248> +##contig=<ID=chr16_KI270728v1_random,length=1872759> +##contig=<ID=chr17_GL000205v2_random,length=185591> +##contig=<ID=chr17_KI270729v1_random,length=280839> +##contig=<ID=chr17_KI270730v1_random,length=112551> +##contig=<ID=chr22_KI270731v1_random,length=150754> +##contig=<ID=chr22_KI270732v1_random,length=41543> +##contig=<ID=chr22_KI270733v1_random,length=179772> +##contig=<ID=chr22_KI270734v1_random,length=165050> +##contig=<ID=chr22_KI270735v1_random,length=42811> +##contig=<ID=chr22_KI270736v1_random,length=181920> +##contig=<ID=chr22_KI270737v1_random,length=103838> +##contig=<ID=chr22_KI270738v1_random,length=99375> +##contig=<ID=chr22_KI270739v1_random,length=73985> +##contig=<ID=chrY_KI270740v1_random,length=37240> +##contig=<ID=chrUn_KI270302v1,length=2274> +##contig=<ID=chrUn_KI270304v1,length=2165> +##contig=<ID=chrUn_KI270303v1,length=1942> +##contig=<ID=chrUn_KI270305v1,length=1472> +##contig=<ID=chrUn_KI270322v1,length=21476> +##contig=<ID=chrUn_KI270320v1,length=4416> +##contig=<ID=chrUn_KI270310v1,length=1201> +##contig=<ID=chrUn_KI270316v1,length=1444> +##contig=<ID=chrUn_KI270315v1,length=2276> +##contig=<ID=chrUn_KI270312v1,length=998> +##contig=<ID=chrUn_KI270311v1,length=12399> +##contig=<ID=chrUn_KI270317v1,length=37690> +##contig=<ID=chrUn_KI270412v1,length=1179> +##contig=<ID=chrUn_KI270411v1,length=2646> +##contig=<ID=chrUn_KI270414v1,length=2489> +##contig=<ID=chrUn_KI270419v1,length=1029> +##contig=<ID=chrUn_KI270418v1,length=2145> +##contig=<ID=chrUn_KI270420v1,length=2321> +##contig=<ID=chrUn_KI270424v1,length=2140> +##contig=<ID=chrUn_KI270417v1,length=2043> +##contig=<ID=chrUn_KI270422v1,length=1445> +##contig=<ID=chrUn_KI270423v1,length=981> +##contig=<ID=chrUn_KI270425v1,length=1884> +##contig=<ID=chrUn_KI270429v1,length=1361> +##contig=<ID=chrUn_KI270442v1,length=392061> +##contig=<ID=chrUn_KI270466v1,length=1233> +##contig=<ID=chrUn_KI270465v1,length=1774> +##contig=<ID=chrUn_KI270467v1,length=3920> +##contig=<ID=chrUn_KI270435v1,length=92983> +##contig=<ID=chrUn_KI270438v1,length=112505> +##contig=<ID=chrUn_KI270468v1,length=4055> +##contig=<ID=chrUn_KI270510v1,length=2415> +##contig=<ID=chrUn_KI270509v1,length=2318> +##contig=<ID=chrUn_KI270518v1,length=2186> +##contig=<ID=chrUn_KI270508v1,length=1951> +##contig=<ID=chrUn_KI270516v1,length=1300> +##contig=<ID=chrUn_KI270512v1,length=22689> +##contig=<ID=chrUn_KI270519v1,length=138126> +##contig=<ID=chrUn_KI270522v1,length=5674> +##contig=<ID=chrUn_KI270511v1,length=8127> +##contig=<ID=chrUn_KI270515v1,length=6361> 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+##contig=<ID=HPV159,length=7443> +##contig=<ID=HPV160,length=7779> +##contig=<ID=HPV161,length=7238> +##contig=<ID=HPV162,length=7214> +##contig=<ID=HPV163,length=7233> +##contig=<ID=HPV164,length=7233> +##contig=<ID=HPV165,length=7129> +##contig=<ID=HPV166,length=7212> +##contig=<ID=HPV167,length=7228> +##contig=<ID=HPV168,length=7204> +##contig=<ID=HPV169,length=7252> +##contig=<ID=HPV170,length=7417> +##contig=<ID=HPV171,length=7261> +##contig=<ID=HPV172,length=7203> +##contig=<ID=HPV173,length=7297> +##contig=<ID=HPV174,length=7359> +##contig=<ID=HPV175,length=7226> +##contig=<ID=HPV178,length=7314> +##contig=<ID=HPV179,length=7228> +##contig=<ID=HPV180,length=7356> +##contig=<ID=HPV184,length=7324> +##contig=<ID=HPV197,length=7278> +##contig=<ID=HPV199,length=7184> +##contig=<ID=HPV-mCG2,length=7152> +##contig=<ID=HPV-mCG3,length=7095> +##contig=<ID=HPV-mCH2,length=7190> +##contig=<ID=HPV-mFD1,length=7286> +##contig=<ID=HPV-mFD2,length=7219> +##contig=<ID=HPV-mFS1,length=7167> +##contig=<ID=HPV-mFi864,length=7247> +##contig=<ID=HPV-mKC5,length=7143> +##contig=<ID=HPV-mKN1,length=7300> +##contig=<ID=HPV-mKN2,length=7299> +##contig=<ID=HPV-mKN3,length=7251> +##contig=<ID=HPV-mL55,length=7177> +##contig=<ID=HPV-mRTRX7,length=7731> +##contig=<ID=HPV-mSD2,length=7300> +##reference=file:///export/job_work_dir/000/551/working/genome.fa +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL +chr22 11603571 . A T . alt_allele_in_normal;clustered_events ECNT=3;HCNT=25;MAX_ED=139;MIN_ED=95;NLOD=82.02;TLOD=6.65 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:404,8:0.019:3:5:0.625:11853,239:196:208 0/0:305,5:0.016:2:3:0.600:8997,153:145:160 +chr22 11603666 . C A . alt_allele_in_normal;clustered_events ECNT=3;HCNT=21;MAX_ED=139;MIN_ED=95;NLOD=189.96;TLOD=17.06 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:1201,19:0.018:8:11:0.579:39536,548:578:623 0/0:1053,33:0.039:13:20:0.606:34747,962:516:537 +chr22 11603710 . G C . alt_allele_in_normal;clustered_events ECNT=3;HCNT=18;MAX_ED=139;MIN_ED=95;NLOD=29.16;TLOD=100.26 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:1454,64:0.045:28:36:0.438:47536,2109:717:737 0/0:1149,124:0.101:57:67:0.460:37571,4096:561:588
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_vcf.vcf Tue Jul 03 06:05:44 2018 -0400 @@ -0,0 +1,2835 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=alt_allele_in_normal,Description="Evidence seen in the normal sample"> +##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor"> +##FILTER=<ID=clustered_read_position,Description="Evidence for somatic variant clusters near the ends of reads"> +##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic"> +##FILTER=<ID=homologous_mapping_event,Description="More than three events were observed in the tumor"> +##FILTER=<ID=multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal"> +##FILTER=<ID=panel_of_normals,Description="Seen in at least 2 samples in the panel of normals"> +##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region"> +##FILTER=<ID=strand_artifact,Description="Evidence for alt allele comes from one read direction only"> +##FILTER=<ID=t_lod_fstar,Description="Tumor does not meet likelihood threshold"> +##FILTER=<ID=triallelic_site,Description="Site filtered because more than two alt alleles pass tumor LOD"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele fraction of the event in the tumor"> +##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the alternate allele"> +##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the alternate allele"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description="Fraction of alt reads indicating OxoG error"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=QSS,Number=A,Type=Integer,Description="Sum of base quality scores for each allele"> +##FORMAT=<ID=REF_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the reference allele"> +##FORMAT=<ID=REF_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the reference allele"> +##GATKCommandLine.MuTect2=<ID=MuTect2,Version=3.8-0-ge9d806836,Date="Wed Apr 11 08:55:44 UTC 2018",Epoch=1523436944508,CommandLineOptions="analysis_type=MuTect2 input_file=[tumor.bam, normal.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[position.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=7 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false cosmic=[] normal_panel=[] dbsnp=(RodBinding name= source=UNBOUND) m2debug=false artifact_detection_mode=false initial_tumor_lod=4.0 initial_normal_lod=0.5 tumor_lod=6.3 normal_lod=2.2 dbsnp_normal_lod=5.5 max_alt_alleles_in_normal_count=1 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=30 strand_artifact_lod=2.0 strand_artifact_power_threshold=0.9 enable_strand_artifact_filter=false enable_clustered_read_position_filter=false pir_median_threshold=10.0 pir_mad_threshold=3.0 debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false debug_read_name=null MQ_filtering_level=20 comp=[] annotation=[DepthPerAlleleBySample, BaseQualitySumPerAlleleBySample, TandemRepeatAnnotator, OxoGReadCounts] excludeAnnotation=[SpanningDeletions] out=/export/galaxy/database/files/001/dataset_1160.dat dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 keepRG=null min_base_quality_score=10 errorCorrectReads=false captureAssemblyFailureBAM=false dontUseSoftClippedBases=false justDetermineActiveRegions=false doNotRunPhysicalPhasing=false maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> +##INFO=<ID=ECNT,Number=1,Type=String,Description="Number of events in this haplotype"> +##INFO=<ID=HCNT,Number=1,Type=String,Description="Number of haplotypes that support this variant"> +##INFO=<ID=MAX_ED,Number=1,Type=Integer,Description="Maximum distance between events in this active region"> +##INFO=<ID=MIN_ED,Number=1,Type=Integer,Description="Minimum distance between events in this active region"> +##INFO=<ID=NLOD,Number=1,Type=String,Description="Normal LOD score"> +##INFO=<ID=PON,Number=1,Type=String,Description="Count from Panel of Normals"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=TLOD,Number=1,Type=String,Description="Tumor LOD score"> +##SAMPLE=<ID=NORMAL,SampleName=normal,File=/export/job_work_dir/000/551/working/normal.bam> +##SAMPLE=<ID=TUMOR,SampleName=tumor,File=/export/job_work_dir/000/551/working/tumor.bam> +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr2,length=242193529> +##contig=<ID=chr3,length=198295559> +##contig=<ID=chr4,length=190214555> +##contig=<ID=chr5,length=181538259> +##contig=<ID=chr6,length=170805979> +##contig=<ID=chr7,length=159345973> +##contig=<ID=chr8,length=145138636> +##contig=<ID=chr9,length=138394717> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr15,length=101991189> +##contig=<ID=chr16,length=90338345> +##contig=<ID=chr17,length=83257441> +##contig=<ID=chr18,length=80373285> +##contig=<ID=chr19,length=58617616> +##contig=<ID=chr20,length=64444167> +##contig=<ID=chr21,length=46709983> +##contig=<ID=chr22,length=50818468> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##contig=<ID=chrM,length=16569> +##contig=<ID=chr1_KI270706v1_random,length=175055> +##contig=<ID=chr1_KI270707v1_random,length=32032> +##contig=<ID=chr1_KI270708v1_random,length=127682> +##contig=<ID=chr1_KI270709v1_random,length=66860> +##contig=<ID=chr1_KI270710v1_random,length=40176> +##contig=<ID=chr1_KI270711v1_random,length=42210> +##contig=<ID=chr1_KI270712v1_random,length=176043> +##contig=<ID=chr1_KI270713v1_random,length=40745> +##contig=<ID=chr1_KI270714v1_random,length=41717> +##contig=<ID=chr2_KI270715v1_random,length=161471> +##contig=<ID=chr2_KI270716v1_random,length=153799> +##contig=<ID=chr3_GL000221v1_random,length=155397> +##contig=<ID=chr4_GL000008v2_random,length=209709> +##contig=<ID=chr5_GL000208v1_random,length=92689> +##contig=<ID=chr9_KI270717v1_random,length=40062> +##contig=<ID=chr9_KI270718v1_random,length=38054> +##contig=<ID=chr9_KI270719v1_random,length=176845> +##contig=<ID=chr9_KI270720v1_random,length=39050> +##contig=<ID=chr11_KI270721v1_random,length=100316> +##contig=<ID=chr14_GL000009v2_random,length=201709> +##contig=<ID=chr14_GL000225v1_random,length=211173> +##contig=<ID=chr14_KI270722v1_random,length=194050> +##contig=<ID=chr14_GL000194v1_random,length=191469> +##contig=<ID=chr14_KI270723v1_random,length=38115> +##contig=<ID=chr14_KI270724v1_random,length=39555> +##contig=<ID=chr14_KI270725v1_random,length=172810> +##contig=<ID=chr14_KI270726v1_random,length=43739> +##contig=<ID=chr15_KI270727v1_random,length=448248> +##contig=<ID=chr16_KI270728v1_random,length=1872759> +##contig=<ID=chr17_GL000205v2_random,length=185591> +##contig=<ID=chr17_KI270729v1_random,length=280839> +##contig=<ID=chr17_KI270730v1_random,length=112551> +##contig=<ID=chr22_KI270731v1_random,length=150754> +##contig=<ID=chr22_KI270732v1_random,length=41543> +##contig=<ID=chr22_KI270733v1_random,length=179772> +##contig=<ID=chr22_KI270734v1_random,length=165050> +##contig=<ID=chr22_KI270735v1_random,length=42811> +##contig=<ID=chr22_KI270736v1_random,length=181920> +##contig=<ID=chr22_KI270737v1_random,length=103838> +##contig=<ID=chr22_KI270738v1_random,length=99375> +##contig=<ID=chr22_KI270739v1_random,length=73985> +##contig=<ID=chrY_KI270740v1_random,length=37240> +##contig=<ID=chrUn_KI270302v1,length=2274> +##contig=<ID=chrUn_KI270304v1,length=2165> +##contig=<ID=chrUn_KI270303v1,length=1942> +##contig=<ID=chrUn_KI270305v1,length=1472> +##contig=<ID=chrUn_KI270322v1,length=21476> +##contig=<ID=chrUn_KI270320v1,length=4416> +##contig=<ID=chrUn_KI270310v1,length=1201> +##contig=<ID=chrUn_KI270316v1,length=1444> +##contig=<ID=chrUn_KI270315v1,length=2276> +##contig=<ID=chrUn_KI270312v1,length=998> +##contig=<ID=chrUn_KI270311v1,length=12399> +##contig=<ID=chrUn_KI270317v1,length=37690> +##contig=<ID=chrUn_KI270412v1,length=1179> +##contig=<ID=chrUn_KI270411v1,length=2646> +##contig=<ID=chrUn_KI270414v1,length=2489> +##contig=<ID=chrUn_KI270419v1,length=1029> +##contig=<ID=chrUn_KI270418v1,length=2145> +##contig=<ID=chrUn_KI270420v1,length=2321> +##contig=<ID=chrUn_KI270424v1,length=2140> +##contig=<ID=chrUn_KI270417v1,length=2043> +##contig=<ID=chrUn_KI270422v1,length=1445> +##contig=<ID=chrUn_KI270423v1,length=981> +##contig=<ID=chrUn_KI270425v1,length=1884> +##contig=<ID=chrUn_KI270429v1,length=1361> +##contig=<ID=chrUn_KI270442v1,length=392061> +##contig=<ID=chrUn_KI270466v1,length=1233> +##contig=<ID=chrUn_KI270465v1,length=1774> +##contig=<ID=chrUn_KI270467v1,length=3920> +##contig=<ID=chrUn_KI270435v1,length=92983> +##contig=<ID=chrUn_KI270438v1,length=112505> +##contig=<ID=chrUn_KI270468v1,length=4055> +##contig=<ID=chrUn_KI270510v1,length=2415> +##contig=<ID=chrUn_KI270509v1,length=2318> +##contig=<ID=chrUn_KI270518v1,length=2186> +##contig=<ID=chrUn_KI270508v1,length=1951> +##contig=<ID=chrUn_KI270516v1,length=1300> +##contig=<ID=chrUn_KI270512v1,length=22689> +##contig=<ID=chrUn_KI270519v1,length=138126> +##contig=<ID=chrUn_KI270522v1,length=5674> +##contig=<ID=chrUn_KI270511v1,length=8127> +##contig=<ID=chrUn_KI270515v1,length=6361> +##contig=<ID=chrUn_KI270507v1,length=5353> +##contig=<ID=chrUn_KI270517v1,length=3253> +##contig=<ID=chrUn_KI270529v1,length=1899> +##contig=<ID=chrUn_KI270528v1,length=2983> +##contig=<ID=chrUn_KI270530v1,length=2168> +##contig=<ID=chrUn_KI270539v1,length=993> +##contig=<ID=chrUn_KI270538v1,length=91309> +##contig=<ID=chrUn_KI270544v1,length=1202> +##contig=<ID=chrUn_KI270548v1,length=1599> +##contig=<ID=chrUn_KI270583v1,length=1400> +##contig=<ID=chrUn_KI270587v1,length=2969> +##contig=<ID=chrUn_KI270580v1,length=1553> +##contig=<ID=chrUn_KI270581v1,length=7046> +##contig=<ID=chrUn_KI270579v1,length=31033> +##contig=<ID=chrUn_KI270589v1,length=44474> +##contig=<ID=chrUn_KI270590v1,length=4685> +##contig=<ID=chrUn_KI270584v1,length=4513> +##contig=<ID=chrUn_KI270582v1,length=6504> +##contig=<ID=chrUn_KI270588v1,length=6158> +##contig=<ID=chrUn_KI270593v1,length=3041> +##contig=<ID=chrUn_KI270591v1,length=5796> +##contig=<ID=chrUn_KI270330v1,length=1652> 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+##contig=<ID=HPV-mFi864,length=7247> +##contig=<ID=HPV-mKC5,length=7143> +##contig=<ID=HPV-mKN1,length=7300> +##contig=<ID=HPV-mKN2,length=7299> +##contig=<ID=HPV-mKN3,length=7251> +##contig=<ID=HPV-mL55,length=7177> +##contig=<ID=HPV-mRTRX7,length=7731> +##contig=<ID=HPV-mSD2,length=7300> +##reference=file:///export/job_work_dir/000/551/working/genome.fa +##FILTER=<ID=NRC,Description="Unable to grab readcounts for variant allele"> +##FILTER=<ID=IRC,Description="Unable to grab any sort of readcount for either the reference or the variant allele"> +##FILTER=<ID=MVC4,Description="Less than 4 high quality reads support the variant"> +##FILTER=<ID=DETP20,Description="Average distance of the variant base to the effective 3' end is less than 0.2"> +##FILTER=<ID=MMQSD50,Description="Difference in average mismatch quality sum between variant and reference supporting reads is greater than 50"> +##FILTER=<ID=MMQS100,Description="The average mismatch quality sum of reads supporting the variant is greater than 100"> +##FILTER=<ID=MQD30,Description="Difference in average mapping quality sum between variant and reference supporting reads is greater than 30"> +##FILTER=<ID=RLD25,Description="Difference in average clipped read length between variant and reference supporting reads is greater than 25"> +##FILTER=<ID=SB1,Description="Reads supporting the variant have less than 0.01 fraction of the reads on one strand, but reference supporting reads are not similarly biased"> +##FILTER=<ID=MVF5,Description="Variant allele frequency is less than 0.05"> +##FILTER=<ID=PB10,Description="Average position on read less than 0.1 or greater than 0.9 fraction of the read length"> +##vcfProcessLog=<InputVCF=</export/galaxy/database/files/001/dataset_1160.dat>, InputVCFSource=<fpfilter>, InputVCFVer=<6.0>, InputVCFParam=<"--vcf-file /export/galaxy/database/files/001/dataset_1160.dat --bam-file /export/galaxy/database/files/001/dataset_1143.dat --bam-index /export/galaxy/database/files/_metadata_files/000/metadata_50.dat --sample TUMOR --reference /export/galaxy/database/files/000/dataset_131.dat --output /export/galaxy/database/files/001/dataset_1518.dat --min-read-pos 0.1 --min-var-freq 0.05 --min-var-count 4 --min-strandedness 0.01 --max-mm-qualsum-diff 50 --max-var-mm-qualsum 100 --max-mapqual-diff 30 --max-readlen-diff 25 --min-var-dist-3 0.2"> InputVCFgeneAnno=<.>> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL +chr22 11603571 . A T . alt_allele_in_normal;clustered_events;SB1;MVF5 ECNT=3;HCNT=25;MAX_ED=139;MIN_ED=95;NLOD=82.02;TLOD=6.65 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:404,8:0.019:3:5:0.625:11853,239:196:208 0/0:305,5:0.016:2:3:0.600:8997,153:145:160 +chr22 11603666 . C A . alt_allele_in_normal;clustered_events;MVF5;MQD30 ECNT=3;HCNT=21;MAX_ED=139;MIN_ED=95;NLOD=189.96;TLOD=17.06 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:1201,19:0.018:8:11:0.579:39536,548:578:623 0/0:1053,33:0.039:13:20:0.606:34747,962:516:537 +chr22 11603710 . G C . alt_allele_in_normal;clustered_events;MQD30 ECNT=3;HCNT=18;MAX_ED=139;MIN_ED=95;NLOD=29.16;TLOD=100.26 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:1454,64:0.045:28:36:0.438:47536,2109:717:737 0/0:1149,124:0.101:57:67:0.460:37571,4096:561:588