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1 #!/usr/bin/perl
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2 use strict;
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3 use Cwd 'abs_path';
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4 use Getopt::Long;
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5 use File::Basename;
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6
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7 my $absPath = abs_path($0);
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8 my $dir = dirname($absPath);
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9 my $lib = "$dir/../lib/";
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10
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11 my $vcf2tsv = "$lib/perl/vcf2tsv.pl";
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12 my $spliteff = "$lib/perl/splitEff.pl";
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13 my $filter = "$lib/perl/filter.pl";
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14 my $plotPng = "$lib/R/plotsPng.R";
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15 my $mkReport = "$lib/perl/mkHtmlReportGalaxy.pl";
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16
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17 my $locifilt = "$dir/../ref/filters/filter.tsv";
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18 my $manifest = "$dir/../ref/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt";
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19
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20 my $canonicals = "$dir/../ref/TSACP/canonicals.tsv";
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21 my $clinvar = "$dir/../ref/filters/clinvar_00-latest.f.vcf";
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22 my $cosmic = "$dir/../ref/filters/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf";
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23 my $cosmicNC = "$dir/../ref/filters/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf";
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24
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25 my $base = undef;
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26 my $vcf = undef;
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27 my $vcfOther = undef;
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28 my $noFilt = undef;
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29 my $noPlot = undef;
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30
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31 my $qc_ann_qual_txt = undef;
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32 my $qc2_ann_txt = undef
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33 my $qc_targets_txt = undef;
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34
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35 GetOptions (
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36 "vcf=s" => \$vcf,
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37 "vcfOther=s" => \$vcfOther,
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38 "output=s" => \$base,
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39 "canonicals=s" => \$canonicals,
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40 "clinvar=s" => \$clinvar,
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41 "cosmic=s" => \$cosmic,
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42 "cosmicNC=s" => \$cosmicNC,
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43 "noFilt" => \$noFilt,
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44 "noPlot" => \$noPlot,
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45 "qc_ann_qual_txt=s" => \$qc_ann_qual_txt,
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46 "qc2_ann_txt=s" => \$qc2_ann_txt,
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47 "qc_targets_txt=s" => \$qc_targets_txt,
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48 )
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49 or die("Error in command line arguments\n");
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50
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51 ## sanity checks
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52 die( "No base name provided [-output]\n" ) unless defined($base) and $base ne '';
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53 die( "No VCF file provided [-vcf]\n" ) unless defined($vcf) and -f $vcf;
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54 die( "Missing input [-qc_ann_qual_txt]\n" ) unless defined($qc_ann_qual_txt) and -f $qc_ann_qual_txt;
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55 die( "Missing input [-qc2_ann_txt]\n" ) unless defined($qc2_ann_txt) and -f $qc2_ann_txt;
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56 die( "Missing input [-qc_targets_txt]\n" ) unless defined($qc_targets_txt) and -f $qc_targets_txt;
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57 die( "Required file does not exists [$canonicals]\n" ) unless -f $canonicals;
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58 die( "Required file does not exists [$clinvar]\n" ) unless -f $clinvar;
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59 die( "Required file does not exists [$cosmic]\n" ) unless -f $cosmic;
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60 die( "Required file does not exists [$cosmicNC]\n" ) unless -f $cosmicNC;
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61
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62
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63 ## Rscript check
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64 my $rscript = `which Rscript`;
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65 chomp $rscript;
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66 if ($rscript !~ /Rscript$/) {
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67 print STDERR "No Rscript present in PATH\n";
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68 exit 1;
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69 }
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70
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71 ## FILTERING
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72 print STDOUT localtime() . " [$$] converting vcf to tsv\n";
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73 system( "$vcf2tsv $vcf > $base\.tsv" );
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74
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75 print STDOUT localtime() . " [$$] splitting vcf columns\n";
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76 system( "$spliteff $base\.tsv Falco >> $base\.res\.tsv" );
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77
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78 if ( defined($vcfOther) ){
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79 print STDOUT localtime() . " [$$] converting vcf to tsv\n";
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80 system( "$vcf2tsv $vcf > $base\.Other\.tsv" );
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81 print STDOUT localtime() . " [$$] splitting vcf columns\n";
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82 system( "$spliteff $base\.Other\.tsv Other >> $base\.res\.tsv" );
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83 }
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84
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85 print STDOUT localtime() . " [$$] filtering data\n";
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86 system( "$filter $base\.res\.tsv $canonicals $clinvar $cosmic $cosmicNC > $base\.res\.filtered\.tsv" );
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87
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88 ## PLOTTING
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89 print STDOUT localtime() . " [$$] Creating plots\n";
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90 system( "Rscript $plotPng $qc_ann_qual_txt $qc2_ann_txt $qc_targets_txt $base\.res\.filtered\.tsv $clinvar $locifilt $base" );
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91
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92 ## REPORTING
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93 print STDOUT localtime() . " [$$] Creating HTML report\n";
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94 system( "perl $mkReport $base" );
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