Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 6:be221fb9cabf
Uploaded
author | yhoogstrate |
---|---|
date | Tue, 17 Dec 2013 05:23:00 -0500 |
parents | 637f78452b3a |
children | 467ace7bd807 |
files | varscan2_from_bam.xml |
diffstat | 1 files changed, 72 insertions(+), 5 deletions(-) [+] |
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--- a/varscan2_from_bam.xml Tue Dec 17 05:03:38 2013 -0500 +++ b/varscan2_from_bam.xml Tue Dec 17 05:23:00 2013 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <tool id="varscan2_from_bam" name="VarScan2 from BAM"> - <description>VarScan2 reading a *.bam file to avoid unncessairy I/O overhead.</description> + <description>VarScan2 (1: directly reading a *.bam file, 2: using parallel mpileup generation, to avoid unncessairy I/O overhead.</description> <requirements> <requirement type="package" version="1.0.19">samtools-mpileup-parallel</requirement> <requirement type="package" version="2.3.6">VarScan</requirement> @@ -13,21 +13,88 @@ The following script is written in the "Cheetah" language: http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html --> - samtools-mpileup-parallel mpileup -t $threads -f $reference_genome + + <!-- + Usage: samtools mpileup [options] in1.bam [in2.bam [...]] + + Input options: + -6 assume the quality is in the Illumina-1.3+ encoding + -A count anomalous read pairs + -B disable BAQ computation + -b FILE list of input BAM filenames, one per line [null] + -C INT parameter for adjusting mapQ; 0 to disable [0] + -d INT max per-BAM depth to avoid excessive memory usage [250] + -E recalculate extended BAQ on the fly thus ignoring existing BQs + -f FILE faidx indexed reference sequence file [null] + -G FILE exclude read groups listed in FILE [null] + -l FILE list of positions (chr pos) or regions (BED) [null] + -M INT cap mapping quality at INT [60] + -r STR region in which pileup is generated [null] + -R ignore RG tags + -q INT skip alignments with mapQ smaller than INT [0] + -Q INT skip bases with baseQ/BAQ smaller than INT [13] + --rf INT required flags: skip reads with mask bits unset [] + --ff INT filter flags: skip reads with mask bits set [] + -t INT Number of parallel threads + + Output options: + -D output per-sample DP in BCF (require -g/-u) + -g generate BCF output (genotype likelihoods) + -O output base positions on reads (disabled by -g/-u) + -s output mapping quality (disabled by -g/-u) + -S output per-sample strand bias P-value in BCF (require -g/-u) + -u generate uncompress BCF output + + SNP/INDEL genotype likelihoods options (effective with `-g' or `-u'): + -e INT Phred-scaled gap extension seq error probability [20] + -F FLOAT minimum fraction of gapped reads for candidates [0.002] + -h INT coefficient for homopolymer errors [100] + -I do not perform indel calling + -L INT max per-sample depth for INDEL calling [250] + -m INT minimum gapped reads for indel candidates [1] + -o INT Phred-scaled gap open sequencing error probability [40] + -p apply -m and -F per-sample to increase sensitivity + -P STR comma separated list of platforms for indels [all] + --> + + <!-- + USAGE: java -jar VarScan.jar mpileup2cns [pileup file] OPTIONS + mpileup file - The SAMtools mpileup file + + OPTIONS: + --min-coverage Minimum read depth at a position to make a call [8] + --min-reads2 Minimum supporting reads at a position to call variants [2] + --min-avg-qual Minimum base quality at a position to count a read [15] + --min-var-freq Minimum variant allele frequency threshold [0.01] + --min-freq-for-hom Minimum frequency to call homozygote [0.75] + --p-value Default p-value threshold for calling variants [99e-02] + --strand-filter Ignore variants with >90% support on one strand [1] + --output-vcf If set to 1, outputs in VCF format + --vcf-sample-list For VCF output, a list of sample names in order, one per line + --variants Report only variant (SNP/indel) positions [0] + --> + + samtools-mpileup-parallel mpileup -t $samtools_threads -f $reference_genome #for $sample in $samples ${sample.mapped_reads} #end for - | java -jar VarScan.v2.2.jar pileup2snp > $output_table + | java -jar VarScan.v2.3.6.jar mpileup2snp $varscan_vcf_output > $output_table </command> - <input type="text" name="threads" value="8" min="1" /> - <inputs> <repeat name="samples" title="Samples" min="1"> <param format="bam,sam" name="mapped_reads" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/> </repeat> <param format="fa,fasta" name="reference_genome" type="data" label="Gene Model Annotations" help="Reference genome (genome.fa) that corresponds to the *.bam file." /> + <input type="text" name="region" label="region in which pileup is generated, leave empy for entire genome" /> + + + <input type="integer" name="samtools_threads" value="8" min="1" title="Samtools: mpileup threads" /> + + + + <input type="boolean" name="varscan_vcf_output" falsevalue=" --output-vcf 0" truevalue=" --output-vcf 1" title="VarScan: VCF output" /> </inputs> <outputs>