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process_alignments_human.pl
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#!/usr/bin/perl
use strict;
use Getopt::Long qw(GetOptions);
use FindBin qw($Bin);
use lib "$Bin/lib";
use Schedule;
use Cluster;
use File::Basename;
my ($patient, $email, $impact, $wes, $svnRev, $pair, $group, $bamgroup, $config, $nosnps, $targets, $ug, $scheduler, $priority_project, $priority_group, $abra, $indelrealigner, $help, $step1, $allSomatic, $scalpel, $somaticsniper, $strelka, $varscan, $virmid);
my $pre = 'TEMP';
my $output = "results";
my $species = 'b37';
my $uID = `/usr/bin/id -u -n`;
chomp $uID;
my $rsync = "/ifs/solres/$uID";
my $tempdir = "/scratch/$uID";
GetOptions ('email=s' => \$email,
'pre=s' => \$pre,
'pair=s' => \$pair,
'patient=s' => \$patient,
'group=s' => \$group,
'config=s' => \$config,
'targets=s' => \$targets,
'species=s' => \$species,
'nosnps' => \$nosnps,
'ug|unifiedgenotyper' => \$ug,
'abra' => \$abra,
'impact' => \$impact,
'wes' => \$wes,
'indelrealigner' => \$indelrealigner,
'step1' => \$step1,
'bamgroup=s' => \$bamgroup,
'scheduler=s' => \$scheduler,
'svnRev=s' => \$svnRev,
'priority_project=s' => \$priority_project,
'priority_group=s' => \$priority_group,
'help' => \$help,
'rsync=s' => \$rsync,
'allsomatic|allSomatic|all_somatic' => \$allSomatic,
'scalpel' => \$scalpel,
'somaticsniper' => \$somaticsniper,
'strelka' => \$strelka,
'varscan' => \$varscan,
'virmid' => \$virmid,
'tempdir=s' => \$tempdir,
'output|out|o=s' => \$output) or exit(1);
if(!$group || !$config || !$scheduler || !$targets || !$bamgroup || $help){
print <<HELP;
USAGE: process_alignments_human.pl -group GROUP -bampgroup BAMBROUP -config CONFIG -scheduler SCHEDULER -targets TARGETS
* GROUP: file listing grouping of samples for realign/recal steps (REQUIRED)
* BAMGROUP: files listing bams to be processed together; every bam for each group on 1 line, comma-separated (required)
* SPECIES: b37, hybrid|xenograft (b37_mm10)
* TARGETS: name of targets assay; will search for targets/baits ilists and targets padded file in $Bin/targets/TARGETS unless given full path to targets directory (REQUIRED)
* CONFIG: file listing paths to programs needed for pipeline; full path to config file needed (REQUIRED)
* SCHEDULER: currently support for SGE and LSF (REQUIRED)
* PAIR: file listing tumor/normal pairing of samples for mutect/maf conversion; if not specified, considered unpaired
* PRE: output prefix (default: TEMP)
* OUTPUT: output results directory (default: results)
* RSYNC: path to rsync data for archive (default: /ifs/solres/USER_ID)
* PRIORITY_PROJECT: sge notion of priority assigned to projects (default: ngs)
* PRIORITY_GROUP: lsf notion of priority assigned to groups (default: Pipeline)
* -nosnps: if no snps to be called; e.g. when only indelrealigned/recalibrated bams needed
* -abra: run abra to realign indels (default)
* -indelrealigner: run GATK indelrealigner (abra runs as default)
* -step1: forece the pipeline to start from the first step in pipeline
* haplotypecaller is default; -ug || -unifiedgenotyper to also make unifiedgenotyper variant calls
* TEMPDIR: temp directory (default: /scratch/$uID)
* ALLSOMATIC: run all somatic callers; mutect/haplotypecaller always run; otherwise -scalpel, -somaticsniper, -strelka, -varscan, -virmid to run them individually
HELP
exit;
}
if(!-d "$rsync"){
die "Can't rsync to $rsync. Please pick a differnt location using the rsync parameter $!";
}
my $curDir = `pwd`;
chomp $curDir;
if($output !~ /^\//){
$output = "$curDir/$output";
}
if($pre =~ /^\d+/){
$pre = "s_$pre";
}
if($wes && $impact){
die "Cannot run as both a wes and an impact. Please select -wes OR -impact";
}elsif(!$wes && !$impact){
die "Must specify to run the project as either -wes or -impact";
}
if($abra && $indelrealigner){
die "Cannot run both abra and gatk indelrealigner $!";
}
elsif(!$abra && !$indelrealigner){
$abra = 1;
}
if($allSomatic){
$scalpel = 1;
$somaticsniper = 1;
$strelka = 1;
$varscan = 1;
$virmid = 1;
}
my $ABRA = '';
my $GATK = '';
my $PICARD = '';
my $MUTECT = '';
my $SAMTOOLS = '';
my $BEDTOOLS = '';
my $SOMATIC_SNIPER = '';
my $VARSCAN = '';
my $VEP = '';
my $STRELKA = '';
my $SCALPEL = '';
my $VIRMID = '';
my $JAVA = '';
my $FACETS_LIB = '';
my $FACETS_SUITE = '';
my $BCFTOOLS= '';
my $TABIX = '';
my $PYTHON = '';
my $PERL = '';
my $B37_FASTA = '';
my $B37_FAI = '';
my $B37_MM10_HYBRID_FASTA = '';
my $B37_MM10_HYBRID_FAI = '';
my $B37_BWA_INDEX = '';
my $B37_MM10_HYBRID_BWA_INDEX = '';
my $HG19_FASTA = '';
my $HG19_FAI = '';
my $HG19_MM10_HYBRID_FASTA = '';
my $HG19_MM10_HYBRID_FAI = '';
my $HG19_BWA_INDEX = '';
my $HG19_MM10_HYBRID_BWA_INDEX = '';
open(CONFIG, "$config") or die "CAN'T OPEN CONFIG FILE $config $!";
while(<CONFIG>){
chomp;
my @conf = split(/\s+/, $_);
if($conf[0] =~ /abra/i){
if(!-e "$conf[1]/abra.jar"){
die "CAN'T FIND GenomeAnalysisTK.jar IN $conf[1] $!";
}
$ABRA = $conf[1];
}
elsif($conf[0] =~ /tabix/i){
if(!-e "$conf[1]/bgzip"){
die "CAN'T FIND tabix IN $conf[1] $!";
}
$TABIX = $conf[1];
}
elsif($conf[0] =~ /bcftools/i){
if(!-e "$conf[1]/bcftools"){
die "CAN'T FIND bcftools IN $conf[1] $!";
}
$BCFTOOLS = $conf[1];
}
elsif($conf[0] =~ /facets_suite/i){
if(!-e "$conf[1]/facets"){
die "CAN'T FIND facets_suite IN $conf[1] $!";
}
$FACETS_SUITE = $conf[1];
}
elsif($conf[0] =~ /facets_lib/i){
if(!-e "$conf[1]/facets"){
die "CAN'T FIND facets_lib IN $conf[1] $!";
}
$FACETS_LIB = $conf[1];
}
elsif($conf[0] =~ /gatk/i){
if(!-e "$conf[1]/GenomeAnalysisTK.jar"){
die "CAN'T FIND GenomeAnalysisTK.jar IN $conf[1] $!";
}
$GATK = $conf[1];
}
elsif($conf[0] =~ /mutect/i){
if(!-e "$conf[1]/muTect.jar"){
die "CAN'T FIND muTect.jar IN $conf[1] $!";
}
$MUTECT = $conf[1];
}
elsif($conf[0] =~ /picard/i){
if(!-e "$conf[1]/picard.jar"){
die "CAN'T FIND picard.jar IN $conf[1] $!";
}
$PICARD = $conf[1];
}
elsif($conf[0] =~ /samtools/i){
if(!-e "$conf[1]/samtools"){
die "CAN'T FIND samtools IN $conf[1] $!";
}
$SAMTOOLS = $conf[1];
}
elsif($conf[0] =~ /bedtools/i){
if(!-e "$conf[1]/bedtools"){
die "CAN'T FIND bedtools IN $conf[1] $!";
}
$BEDTOOLS = $conf[1];
}
elsif($conf[0] =~ /somaticsniper/i){
if(!-e "$conf[1]/bam-somaticsniper"){
die "CAN'T FIND bam-somaticsniper IN $conf[1] $!";
}
$SOMATIC_SNIPER = $conf[1];
}
elsif($conf[0] =~ /varscan/i){
if(!-e "$conf[1]/VarScan.jar"){
die "CAN'T FIND VarScan.jar IN $conf[1] $!";
}
$VARSCAN = $conf[1];
}
elsif($conf[0] =~ /^vep/i){
if(!-e "$conf[1]/variant_effect_predictor.pl"){
die "CAN'T FIND VEP IN $conf[1] $!";
}
$VEP = $conf[1];
}
elsif($conf[0] =~ /strelka/i){
if(!-e "$conf[1]/bin/configureStrelkaWorkflow.pl"){
die "CAN'T FIND bin/configureStrelkaWorkflow.pl IN $conf[1] $!";
}
$STRELKA = $conf[1];
}
elsif($conf[0] =~ /scalpel/i){
if(!-e "$conf[1]/scalpel"){
die "CAN'T FIND scalpel IN $conf[1] $!";
}
$SCALPEL = $conf[1];
}
elsif($conf[0] =~ /virmid/i){
if(!-e "$conf[1]/Virmid.jar"){
die "CAN'T FIND Virmid.jar IN $conf[1] $!";
}
$VIRMID = $conf[1];
}
elsif($conf[0] =~ /java/i){
if(!-e "$conf[1]/java"){
die "CAN'T FIND java IN $conf[1] $!";
}
$JAVA = $conf[1];
my $path_tmp = $ENV{'PATH'};
$ENV{'PATH'} = "$conf[1]:$path_tmp";
}
elsif($conf[0] =~ /perl/i){
if(!-e "$conf[1]/perl"){
die "CAN'T FIND perl IN $conf[1] $!";
}
$PERL = $conf[1];
my $path_tmp = $ENV{'PATH'};
$ENV{'PATH'} = "$conf[1]:$path_tmp";
}
elsif($conf[0] =~ /python/i){
if(!-e "$conf[1]/python"){
die "CAN'T FIND python IN $conf[1] $!";
}
$PYTHON = $conf[1];
my $path_tmp = $ENV{'PATH'};
$ENV{'PATH'} = "$conf[1]:$path_tmp";
}
elsif($conf[0] =~ /^r$/i){
if(!-e "$conf[1]/R"){
die "CAN'T FIND R IN $conf[1] $!";
}
my $path_tmp = $ENV{'PATH'};
$ENV{'PATH'} = "$conf[1]:$path_tmp";
}
elsif($conf[0] =~ /b37_fasta/i){
if(!-e "$conf[1]"){
if($species =~ /human|^b37$/i){
die "CAN'T FIND $conf[1] $!";
}
}
$B37_FASTA = $conf[1];
}
elsif($conf[0] =~ /b37_fai/i){
if(!-e "$conf[1]"){
if($species =~ /human|^b37$/i){
die "CAN'T FIND $conf[1] $!";
}
}
$B37_FAI = $conf[1];
}
elsif($conf[0] =~ /b37_mm10_hybrid_fasta/i){
if(!-e "$conf[1]"){
if($species =~ /hybrid|xenograft|b37_mm10/i){
die "CAN'T FIND $conf[1] $!";
}
}
$B37_MM10_HYBRID_FASTA = $conf[1];
}
elsif($conf[0] =~ /b37_mm10_hybrid_fai/i){
if(!-e "$conf[1]"){
if($species =~ /hybrid|xenograft|b37_mm10/i){
die "CAN'T FIND $conf[1] $!";
}
}
$B37_MM10_HYBRID_FAI = $conf[1];
}
elsif($conf[0] =~ /b37_bwa_index/i){
if(!-e "$conf[1]\.bwt" || !-e "$conf[1]\.pac" || !-e "$conf[1]\.ann" || !-e "$conf[1]\.amb" || !-e "$conf[1]\.sa"){
if($species =~ /^b37$/i){
die "CAN'T FIND ALL NECESSARY BWA INDEX FILES FOR B37 WITH PREFIX $conf[1] $!";
}
}
$B37_BWA_INDEX = $conf[1];
}
elsif($conf[0] =~ /b37_mm10_hybrid_bwa_index/i){
if(!-e "$conf[1]\.bwt" || !-e "$conf[1]\.pac" || !-e "$conf[1]\.ann" || !-e "$conf[1]\.amb" || !-e "$conf[1]\.sa"){
if($species =~ /hybrid|xenograft|b37_mm10/i){
die "CAN'T FIND ALL NECESSARY BWA INDEX FILES FOR b37-MM10 HYBRID WITH PREFIX $conf[1] $!";
}
}
$B37_MM10_HYBRID_BWA_INDEX = $conf[1];
}
elsif($conf[0] =~ /hg19_fasta/i){
if(!-e "$conf[1]"){
if($species =~ /^hg19$/i){
die "CAN'T FIND $conf[1] $!";
}
}
$HG19_FASTA = $conf[1];
}
elsif($conf[0] =~ /hg19_fai/i){
if(!-e "$conf[1]"){
if($species =~ /^hg19$/i){
die "CAN'T FIND $conf[1] $!";
}
}
$HG19_FAI = $conf[1];
}
elsif($conf[0] =~ /hg19_mm10_hybrid_fasta/i){
if(!-e "$conf[1]"){
if($species =~ /hg19_mm10/i){
die "CAN'T FIND $conf[1] $!";
}
}
$HG19_MM10_HYBRID_FASTA = $conf[1];
}
elsif($conf[0] =~ /hg19_mm10_hybrid_fai/i){
if(!-e "$conf[1]"){
if($species =~ /hg19_mm10/i){
die "CAN'T FIND $conf[1] $!";
}
}
$HG19_MM10_HYBRID_FAI = $conf[1];
}
elsif($conf[0] =~ /hg19_bwa_index/i){
if(!-e "$conf[1]\.bwt" || !-e "$conf[1]\.pac" || !-e "$conf[1]\.ann" || !-e "$conf[1]\.amb" || !-e "$conf[1]\.sa"){
if($species =~ /^hg19$/i){
die "CAN'T FIND ALL NECESSARY BWA INDEX FILES FOR HG19 WITH PREFIX $conf[1] $!";
}
}
$HG19_BWA_INDEX = $conf[1];
}
elsif($conf[0] =~ /hg19_mm10_hybrid_bwa_index/i){
if(!-e "$conf[1]\.bwt" || !-e "$conf[1]\.pac" || !-e "$conf[1]\.ann" || !-e "$conf[1]\.amb" || !-e "$conf[1]\.sa"){
if($species =~ /hg19_mm10/i){
die "CAN'T FIND ALL NECESSARY BWA INDEX FILES FOR HG19-MM10 HYBRID WITH PREFIX $conf[1] $!";
}
}
$HG19_MM10_HYBRID_BWA_INDEX = $conf[1];
}
}
close CONFIG;
my $REF_SEQ = '';
my $REF_FAI = '';
my $BWA_INDEX = '';
my $DB_SNP = "";
my $ExAC_VCF = '';
my $FACETS_DB_SNP = "";
my $MILLS_1000G = '';
my $HAPMAP = '';
my $OMNI_1000G = '';
my $PHASE1_SNPS_1000G = '';
my $COSMIC = '';
my $COSMIC_HOTSPOTS = '';
if($species =~ /^b37$|human/i){
$REF_SEQ = "$B37_FASTA";
$REF_FAI = "$B37_FAI";
$BWA_INDEX = "$B37_BWA_INDEX";
$DB_SNP = "$Bin/data/b37/dbsnp_138.b37.excluding_sites_after_129.vcf";
$ExAC_VCF = "$VEP/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz";
$FACETS_DB_SNP = "$Bin/data/b37/dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf";
$MILLS_1000G = "$Bin/data/b37/Mills_and_1000G_gold_standard.indels.b37.vcf";
$HAPMAP = "$Bin/data/b37/hapmap_3.3.b37.vcf";
$OMNI_1000G = "$Bin/data/b37/1000G_omni2.5.b37.vcf";
$PHASE1_SNPS_1000G = "$Bin/data/b37/1000G_phase1.snps.high_confidence.b37.vcf";
$COSMIC = "$Bin/data/b37/CosmicCodingMuts_v67_b37_20131024__NDS.vcf";
$COSMIC_HOTSPOTS = "$Bin/data/b37/dmp_cosmic_for_hotspots.vcf";
if (! -s $ExAC_VCF ){
die "$ExAC_VCF not present! $!";
}
}
elsif($species =~ /hybrid|xenograft|b37_mm10/i){
$REF_SEQ = "$B37_MM10_HYBRID_FASTA";
$REF_FAI = "$B37_MM10_HYBRID_FAI";
$BWA_INDEX = "$B37_MM10_HYBRID_BWA_INDEX";
$ExAC_VCF = "$VEP/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz";
$DB_SNP = "$Bin/data/b37/dbsnp_138.b37.excluding_sites_after_129.vcf";
$FACETS_DB_SNP = "$Bin/data/b37/dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf";
$MILLS_1000G = "$Bin/data/b37/Mills_and_1000G_gold_standard.indels.b37.vcf";
$HAPMAP = "$Bin/data/b37/hapmap_3.3.b37.vcf";
$OMNI_1000G = "$Bin/data/b37/1000G_omni2.5.b37.vcf";
$PHASE1_SNPS_1000G = "$Bin/data/b37/1000G_phase1.snps.high_confidence.b37.vcf";
$COSMIC = "$Bin/data/b37/CosmicCodingMuts_v67_b37_20131024__NDS.vcf";
$COSMIC_HOTSPOTS = "$Bin/data/b37/dmp_cosmic_for_hotspots.vcf";
if (! -s $ExAC_VCF ){
die "$ExAC_VCF not present! $!";
}
}
elsif($species =~ /^hg19$/i){
die "hg19 is no longer supported in the variants pipeline";
$REF_SEQ = "$HG19_FASTA";
$REF_FAI = "$HG19_FAI";
$BWA_INDEX = "$HG19_BWA_INDEX";
$DB_SNP = "$Bin/data/hg19/dbsnp_138.hg19.excluding_sites_after_129.vcf";
$FACETS_DB_SNP = "$Bin/data/hg19/dbsnp_137.hg19__RmDupsClean__plusPseudo50__DROP_SORT.vcf";
$MILLS_1000G = "$Bin/data/hg19/Mills_and_1000G_gold_standard.indels.hg19.vcf";
$HAPMAP = "$Bin/data/hg19/hapmap_3.3.hg19.vcf";
$OMNI_1000G = "$Bin/data/hg19/1000G_omni2.5.hg19.vcf";
$PHASE1_SNPS_1000G = "$Bin/data/hg19/1000G_phase1.snps.high_confidence.hg19.vcf";
$COSMIC = "$Bin/data/hg19/CosmicCodingMuts_v67_20131024.vcf";
$COSMIC_HOTSPOTS = "$Bin/data/b37/dmp_cosmic_for_hotspots.vcf";
}
elsif($species =~ /hg19_mm10/i){
die "hg19 is no longer supported in the variants pipeline";
$REF_SEQ = "$HG19_MM10_HYBRID_FASTA";
$REF_FAI = "$HG19_MM10_HYBRID_FAI";
$BWA_INDEX = "$HG19_MM10_HYBRID_BWA_INDEX";
$DB_SNP = "$Bin/data/hg19/dbsnp_138.hg19.excluding_sites_after_129.vcf";
$FACETS_DB_SNP = "$Bin/data/hg19/dbsnp_137.hg19__RmDupsClean__plusPseudo50__DROP_SORT.vcf";
$MILLS_1000G = "$Bin/data/hg19/Mills_and_1000G_gold_standard.indels.hg19.vcf";
$HAPMAP = "$Bin/data/hg19/hapmap_3.3.hg19.vcf";
$OMNI_1000G = "$Bin/data/hg19/1000G_omni2.5.hg19.vcf";
$PHASE1_SNPS_1000G = "$Bin/data/hg19/1000G_phase1.snps.high_confidence.hg19.vcf";
$COSMIC = "$Bin/data/hg19/CosmicCodingMuts_v67_20131024.vcf";
$COSMIC_HOTSPOTS = "$Bin/data/b37/dmp_cosmic_for_hotspots.vcf";
}
elsif($species !~ /b37|hybrid|xenograft|b37_mm10/){
die "ONLY SUPPORT FOR b37 or hybrd|xenograft assemblies $!";
}
### make sure all markdup bam files are there before proceeding
open(BGR, "$bamgroup") || die "CAN'T OPEN GROUPING FILE OF MARKDUP BAMS $bamgroup $!";
while(<BGR>){
chomp;
my @bgro = split(/\s+/, $_);
my @bgr = split(/,/, $bgro[1]);
foreach my $bg (@bgr){
if(!-e $bg){
die "file $bg does not exist";
}
}
}
close BGR;
my $targets_bed_padded = "$Bin/targets/$targets/$targets\_targets_plus5bp.bed";
my $target_design = "$Bin/targets/$targets/$targets\__DESIGN.berger";
### std normals prefix; $targets\_norms_title.txt and $targets\_norms\_ALL_intervalnomapqcoverage_loess.txt required
my $target_std_normals = "$Bin/targets/$targets/StdNormals/$targets\_norms";
if(-d $targets){
my @path = split(/\//, $targets);
my $assay = pop @path;
$targets_bed_padded = "$targets/$assay\_targets_plus5bp.bed";
$target_design = "$targets/$assay\__DESIGN.berger";
if($abra){
$target_std_normals = "$targets/StdNormals/$assay\_abra_norms";
}
else{
$target_std_normals = "$targets/StdNormals/$assay\_gatk_norms";
}
}
if(!-e "$targets_bed_padded"){
die "CAN'T LOCATE $targets_bed_padded FOR $targets; REQUIRED FOR SCALPEL $!";
}
my $multipleTargets = '';
### NOTE: THERE SEEMS TO BE SOMETHING WRONG WITH DIPS IN COVERAGE AT TARGET BOUNDARY
### SO NOT USING THE TARGETS FOR ANALYSI
###if($target_bed){
### if(!-e $target_bed){
### die "target file $target_bed cannot be found $!";
### }
### $multipleTargets = "-L $target_bed --interval_set_rule INTERSECTION";
###}
my @ref_chr = ();
open(FAI, "$REF_FAI") or die "CAN'T OPEN FAI FILE $REF_FAI $!";
while(<FAI>){
chomp;
my @line = split(/\s+/, $_);
push @ref_chr, $line[0];
}
close FAI;
if($allSomatic){
$scalpel = 1;
$somaticsniper = 1;
$strelka = 1;
$varscan = 1;
$virmid = 1;
}
my $count = 0;
my %inputFiles = ();
my %processedBams = ();
my @finalBams = ();
my %ran_pr_glob = 0;
my @prg_jids = ();
my $ran_ssf = 0;
my @ssf_jids = ();
my @all_jids = ();
if(!-d $output){
mkdir("$output", 0775) or die "Can't make $output";
}
if(!-d "$output/intFiles"){
mkdir("$output/intFiles", 0775) or die "Can't make $output/intFiles";
}
if(!-d "$output/alignments"){
mkdir("$output/alignments", 0775) or die "Can't make $output/alignments";
}
if(!-d "$output/progress"){
mkdir("$output/progress", 0775) or die "Can't make $output/progress";
}
if(!-d $tempdir){
mkdir("$tempdir", 0775) or die "Can't make $tempdir";
}
my %addParams = (scheduler => "$scheduler", runtime => "500", priority_project=> "$priority_project", priority_group=> "$priority_group", queues => "lau.q,lcg.q,nce.q", rerun => "1", iounits => "1");
my $additionalParams = Schedule::additionalParams(%addParams);
open(IN, "$bamgroup") || die "CAN'T OPEN GROUPING FILE OF MARKDUP BAMS $bamgroup $!";
while(<IN>){
chomp;
my @gpair = split(/\s+/, $_);
my @pair = split(/,/, $gpair[1]);
my @pins = ();
foreach my $pai (@pair){
my @sp = split(/intFiles\//, $pai);
my @sn = split(/\//, $sp[1]);
if($inputFiles{$pai}){
### IN CASE A FILE SHOWS UP MULTIPLE TIMES DUE TO BEING IN MULTIPLE COMPARISONS AND WASN'T COLLAPSED e.g. MET ANALYSIS
### THIS MAKES SURE THAT A FILE ISN'T INCLUDED MULTIPLE TIMES IN PROCESSING
next;
}
push @pins, "-I $pai";
$inputFiles{$pai} = 1;
## store final bams for post-recalibration stats
my $samp = $sn[0];
push @finalBams, "$output/alignments/$pre\_indelRealigned_recal_$samp.bam";
}
if(scalar(@pins) == 0){
### IN CASE ALL ENTRIES IN LINE CONTAINED BAMS ALREADY SEEN IN OTHER COMPARISONS
next;
}
my $bgroup = join(" ", @pins);
my @indelBams = ();
my $ran_ir = 0;
my @ir_jids = ();
foreach my $c (@ref_chr){
if($abra){
my @inBams = ();
my @outBams = ();
my $ran_chr_split_index = 0;
my @chri_jids = ();
foreach my $pin (@pins){
my @inB = split(/\s+/, $pin);
my @bpath = split(/\//, $inB[1]);
my $boi = pop @bpath;
my $ran_chr_split = 0;
my $chrsj = '';
if(!-e "$output/progress/$pre\_$uID\_$boi\_$c\.done" || $step1){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$boi\_$c", cpu => "1", mem => "10", cluster_out => "$output/progress/$pre\_$uID\_$boi\_$c\.log");
my $standardParams = Schedule::queuing(%stdParams);
my %addParams = (scheduler => "$scheduler", runtime => "500", priority_project=> "$priority_project", priority_group=> "$priority_group", rerun => "1", iounits => "2");
my $additionalParams = Schedule::additionalParams(%addParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $SAMTOOLS/samtools view -b -o $inB[1]\_$c\.bam $inB[1] $c`;
$chrsj = "$pre\_$uID\_$boi\_$c";
`/bin/touch $output/progress/$pre\_$uID\_$boi\_$c\.done`;
$ran_chr_split = 1;
}
if(!-e "$output/progress/$pre\_$uID\_$boi\_$c\_INDEX.done" || $ran_chr_split){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$boi\_$c\_INDEX", job_hold => "$chrsj", cpu => "1", mem => "10", cluster_out => "$output/progress/$pre\_$uID\_$boi\_$c\_INDEX.log");
my $standardParams = Schedule::queuing(%stdParams);
my %addParams = (scheduler => "$scheduler", runtime => "500", priority_project=> "$priority_project", priority_group=> "$priority_group", rerun => "1", iounits => "2");
my $additionalParams = Schedule::additionalParams(%addParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $SAMTOOLS/samtools index $inB[1]\_$c\.bam`;
push @chri_jids, "$pre\_$uID\_$boi\_$c\_INDEX";
`/bin/touch $output/progress/$pre\_$uID\_$boi\_$c\_INDEX.done`;
$ran_chr_split_index = 1;
}
push @inBams, "$inB[1]\_$c\.bam";
push @outBams, "$inB[1]\_$c\_ABRA.bam";
}
my $aiBams = join(",", @inBams);
my $aoBams = join(",", @outBams);
my $cij = join(",", @chri_jids);
my $ran_abra = 0;
my $abra_jid = '';
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_$c\_ABRA.done" || $ran_chr_split_index){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_$c\_ABRA", job_hold => "$cij", cpu => "12", mem => "90", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_$c\_ABRA.log");
my $standardParams = Schedule::queuing(%stdParams);
my %addParams = (scheduler => "$scheduler", runtime => "500", priority_project=> "$priority_project", priority_group=> "$priority_group", rerun => "1", iounits => "4");
my $additionalParams = Schedule::additionalParams(%addParams);
###`$standardParams->{submit} $standardParams->{job_name} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx100g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $ABRA/abra.jar --in $aiBams --out $aoBams --ref $REF_SEQ --bwa-ref $BWA_INDEX --targets $ABRA_TARGETS --working $output/intFiles/abra_$gpair[0] --threads 12`;
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $PERL/perl $Bin/abra_wrapper.pl -inBams $aiBams -outBams $aoBams -refSeq $REF_SEQ -bwaRef $BWA_INDEX -targets $targets_bed_padded -working $output/intFiles/abra_$gpair[0]\_$c -config $config -log $output/progress/$pre\_$uID\_$gpair[0]\_$c\_ABRA_WRAPPER.log`;
$abra_jid = "$pre\_$uID\_$gpair[0]\_$c\_ABRA";
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_$c\_ABRA.done`;
$ran_abra = 1;
}
my $ran_fm = 0;
my @fm_jids = ();
my @fm_bams = ();
my $bcount = 0;
my $bcount = 0;
foreach my $outBam (@outBams){
$bcount++;
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_$bcount\_$c\_FIXMATE.done" || $ran_abra){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_$bcount\_$c\_FIXMATE", job_hold => "$abra_jid", cpu => "1", mem => "50", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_$bcount\_$c\_FIXMATE.log");
my $standardParams = Schedule::queuing(%stdParams);
my %addParams = (scheduler => "$scheduler", runtime => "500", priority_project=> "$priority_project", priority_group=> "$priority_group", queues => "lau.q,lcg.q,nce.q", rerun => "1", iounits => "5");
my $additionalParams = Schedule::additionalParams(%addParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx50g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $PICARD/picard.jar FixMateInformation I=$outBam O=$outBam\_FM.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT TMP_DIR=$tempdir MAX_RECORDS_IN_RAM=5000000 CREATE_INDEX=true`;
push @fm_jids, "$pre\_$uID\_$gpair[0]\_$bcount\_$c\_FIXMATE";
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_$bcount\_$c\_FIXMATE.done`;
$ran_fm = 1;
}
push @fm_bams, "I=$outBam\_FM.bam";
}
my $fmj = join(",", @fm_jids);
my $fmb = join(" ", @fm_bams);
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_MERGE_$c\_FM.done" || $ran_fm){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_MERGE_$c\_FM", job_hold => "$fmj", cpu => "8", mem => "30", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_MERGE_$c\_FM.log");
my $standardParams = Schedule::queuing(%stdParams);
my %addParams = (scheduler => "$scheduler", runtime => "500", priority_project=> "$priority_project", priority_group=> "$priority_group", queues => "lau.q,lcg.q,nce.q", rerun => "1", iounits => "10");
my $additionalParams = Schedule::additionalParams(%addParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx30g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $PICARD/picard.jar MergeSamFiles $fmb O=$output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigned.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT TMP_DIR=$tempdir CREATE_INDEX=true USE_THREADING=false MAX_RECORDS_IN_RAM=5000000`;
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_MERGE_$c\_FM.done`;
push @ir_jids, "$pre\_$uID\_$gpair[0]\_MERGE_$c\_FM";
$ran_ir = 1;
}
}
elsif($indelrealigner){
my $ran_rtc = 0;
my $rtc_jid = '';
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_$c\_RTC.done" || $step1){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_$c\_RTC", cpu => "10", mem => "5", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_$c\_RTC.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx5g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R $REF_SEQ -L $c $multipleTargets --known $MILLS_1000G --known $DB_SNP -S LENIENT -nt 10 -rf BadCigar --downsampling_type NONE --out $output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigner.intervals $bgroup`;
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_$c\_RTC.done`;
$rtc_jid = "$pre\_$uID\_$gpair[0]\_$c\_RTC";
$ran_rtc = 1;
}
### seems to randomly have issues with file locking timeout on the m nodes so not submitting to it anymore
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_$c\_IR.done" || $ran_rtc){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_$c\_IR", job_hold => "$rtc_jid", cpu => "1", mem => "15", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_$c\_IR.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx15g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T IndelRealigner -R $REF_SEQ -L $c $multipleTargets --knownAlleles $MILLS_1000G --knownAlleles $DB_SNP -S LENIENT --targetIntervals $output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigner.intervals --maxReadsForRealignment 500000 --maxReadsInMemory 3000000 --maxReadsForConsensuses 500000 -rf BadCigar --out $output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigned.bam $bgroup`;
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_$c\_IR.done`;
push @ir_jids, "$pre\_$uID\_$gpair[0]\_$c\_IR";
$ran_ir = 1;
}
}
else{
die "no indel realinger chosen #!";
}
push @indelBams, "-I $output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigned.bam";
}
my $irBams = join(" ", @indelBams);
my $ran_br = 0;
my $brj = '';
my $irj = join(",", @ir_jids);
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_BR.done" || $ran_ir){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_BR", job_hold => "$irj", cpu => "12", mem => "40", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_BR.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx30g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -l INFO -R $REF_SEQ -S LENIENT --knownSites $DB_SNP --knownSites $MILLS_1000G --knownSites $HAPMAP --knownSites $OMNI_1000G --knownSites $PHASE1_SNPS_1000G --covariate ContextCovariate --covariate CycleCovariate --covariate QualityScoreCovariate --covariate ReadGroupCovariate -rf BadCigar --num_cpu_threads_per_data_thread 12 --out $output/intFiles/$pre\_$gpair[0]\_recal_data.grp $irBams`;
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_BR.done`;
$brj = "$pre\_$uID\_$gpair[0]\_BR";
$ran_br = 1;
}
my @indelRecalBams1 = ();
my $ran_pr = 0;
my @pr_jids = ();
foreach my $c (@ref_chr){
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_$c\_PR.done" || $ran_br){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_$c\_PR", job_hold => "$brj", cpu => "6", mem => "30", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_$c\_PR.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx30g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T PrintReads -R $REF_SEQ -L $c $multipleTargets --emit_original_quals -BQSR $output/intFiles/$pre\_$gpair[0]\_recal_data.grp --num_cpu_threads_per_data_thread 6 -rf BadCigar --downsampling_type NONE --out $output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigned_recal.bam -I $output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigned.bam`;
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_$c\_PR.done`;
push @pr_jids, "$pre\_$uID\_$gpair[0]\_$c\_PR";
push @prg_jids, "$pre\_$uID\_$gpair[0]\_$c\_PR";
$ran_pr = 1;
$ran_pr_glob{"$c"} = 1;
}
push @indelRecalBams1, "I=$output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigned_recal.bam";
push @{$processedBams{"$c"}}, "-I $output/intFiles/$pre\_$gpair[0]\_$c\_indelRealigned_recal.bam";
}
my $irBams1 = join(" ", @indelRecalBams1);
my $ran_m = 0;
my $prj = join(",", @pr_jids);
my @merge_jids = ();
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_MERGE_PR.done" || $ran_pr){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_MERGE_PR", job_hold => "$prj", cpu => "8", mem => "30", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_MERGE_PR.log");
my $standardParams = Schedule::queuing(%stdParams);
my %addParams = (scheduler => "$scheduler", runtime => "500", priority_project=> "$priority_project", priority_group=> "$priority_group", queues => "lau.q,lcg.q,nce.q", rerun => "1", iounits => "10");
my $additionalParams = Schedule::additionalParams(%addParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx30g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $PICARD/picard.jar MergeSamFiles $irBams1 O=$output/intFiles/$pre\_$gpair[0]\_indelRealigned_recal.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT TMP_DIR=$tempdir CREATE_INDEX=true USE_THREADING=false MAX_RECORDS_IN_RAM=5000000`;
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_MERGE_PR.done`;
push @merge_jids, "$pre\_$uID\_$gpair[0]\_MERGE_PR";
$ran_m = 1;
}
my $mj = join(",", @merge_jids);
if(!-e "$output/progress/$pre\_$uID\_$gpair[0]\_SSF.done" || $ran_m){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$gpair[0]\_SSF", job_hold => "$mj", cpu => "1", mem => "10", cluster_out => "$output/progress/$pre\_$uID\_$gpair[0]\_SSF.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx10g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T SplitSamFile -R $REF_SEQ -I $output/intFiles/$pre\_$gpair[0]\_indelRealigned_recal.bam --outputRoot $output/alignments/$pre\_indelRealigned_recal_`;
`/bin/touch $output/progress/$pre\_$uID\_$gpair[0]\_SSF.done`;
push @ssf_jids, "$pre\_$uID\_$gpair[0]\_SSF";
$ran_ssf = 1;
}
}
my $ssfj = join(",", @ssf_jids);
push @all_jids, @ssf_jids;
my @mq_metrics_jid = ();
my @ad_jids = ();
my $ran_mqm = 0;
my $ran_ad = 0;
foreach my $finalBam (@finalBams){
my @sn = split(/\//, $finalBam);
my $samp = $sn[-1];
$samp =~ s/\.bam//g;
$samp =~ s/$pre\_indelRealigned_recal_//g;
if(!-e "$output/progress/$pre\_$uID\_MQ_METRICS_$samp\.done" || $ran_ssf){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_MQ_METRICS_$samp", job_hold => "$ssfj", cpu => "1", mem => "10", cluster_out => "$output/progress/$pre\_$uID\_MQ_METRICS_$samp\.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Djava.io.tmpdir=$tempdir -jar $PICARD/picard.jar MeanQualityByCycle INPUT=$finalBam OUTPUT=$output/intFiles/$pre\_MeanQualityByCycle_$samp.txt CHART_OUTPUT=$output/intFiles/$pre\_MeanQualityByCycle_$samp.pdf REFERENCE_SEQUENCE=$REF_SEQ VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true TMP_DIR=$tempdir`;
push @mq_metrics_jid, "$pre\_$uID\_MQ_METRICS_$samp";
`/bin/touch $output/progress/$pre\_$uID\_MQ_METRICS_$samp\.done`;
$ran_mqm = 1;
}
## generate *alleledepth file for 'hotspots in normals' qc
if(!-e "$output/progress/$pre\_$uID\_MUT_AD_$samp\.done" || $ran_ssf){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_MUT_AD_$samp", job_hold => "$ssfj", cpu => "1", mem => "2", cluster_out => "$output/progress/$pre\_$uID\_MUT_AD_$samp\.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $PERL/perl $Bin/qc/dmp_genotype_allele.pl -fmv $COSMIC_HOTSPOTS -bam $finalBam -rf $REF_SEQ -s $SAMTOOLS -b $BEDTOOLS -o $output/intFiles/$samp -of $pre\_indelRealigned_recal_$samp\.mpileup.alleledepth -mof $pre\_indelRealigned_recal_$samp\.mpileup`;
push @ad_jids, "$pre\_$uID\_MUT_AD_$samp";
`/bin/touch $output/progress/$pre\_$uID\_MUT_AD_$samp\.done`;
$ran_ad = 1;
}
}
my $mqmj = join(",", @mq_metrics_jid);
my $ran_mmqm = 0;
if(!-e "$output/progress/$pre\_$uID\_MERGE_MQ.done" || $ran_mqm){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_MERGE_MQ", job_hold => "$mqmj", cpu => "1", mem => "1", cluster_out => "$output/progress/$pre\_$uID\_MERGE_MQ.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $PYTHON/python $Bin/qc/mergeMeanQualityHistograms.py $output '*_MeanQualityByCycle_*.txt' $output/metrics/$pre\_post_recal_MeanQualityByCycle.txt $output/metrics/$pre\_pre_recal_MeanQualityByCycle.txt`;
`/bin/touch $output/progress/$pre\_$uID\_MERGE_MQ.done`;
push @all_jids, "$pre\_$uID\_MERGE_MQ";
$ran_mmqm = 1;
}
my $adj = join(",", @ad_jids);
my $ran_hn = 0;
if(!-e "$output/progress/$pre\_$uID\_HOTSPOTS_NORMALS.done" || $ran_ad){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_HOTSPOTS_NORMALS", job_hold => "$adj", cpu => "1", mem => "1", cluster_out => "$output/progress/$pre\_$uID\_HOTSPOTS_NORMALS.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $PYTHON/python $Bin/qc/hotspots_in_normals.py $output/intFiles '*.alleledepth' $COSMIC_HOTSPOTS $pair $output/metrics/$pre\_HotspotsInNormals.txt`;
`/bin/touch $output/progress/$pre\_$uID\_HOTSPOTS_NORMALS.done`;
push @all_jids, "$pre\_$uID\_HOTSPOTS_NORMALS";
$ran_hn = 1;
}
my $allj = join(",", @all_jids);
#if(!-e "$output/progress/$pre\_$uID\_RSYNC_1.done" || $ran_ssf || $ran_mmqm || $ran_hn){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_RSYNC_1", job_hold => "$allj", cpu => "1", mem => "1", cluster_out => "$output/progress/$pre\_$uID\_RSYNC_1.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams /usr/bin/rsync -azvP --exclude 'intFiles' --exclude 'progress' --exclude 'variants' --exclude 'metrics' $curDir $rsync`;
push @all_jids, "$pre\_$uID\_RSYNC_1";
`/bin/touch $output/progress/$pre\_$uID\_RSYNC_1.done`;
#}
if($nosnps){
exit(0);
}
if(!-d "$output/variants"){
mkdir("$output/variants", 0775) or die "Can't make $output/variants";
}
if(!-d "$output/variants/snpsIndels"){
mkdir("$output/variants/snpsIndels", 0775) or die "Can't make $output/variants/snpsIndels";
}
if(!-d "$output/variants/snpsIndels/haplotypecaller"){
mkdir("$output/variants/snpsIndels/haplotypecaller", 0775) or die "Can't make $output/variants/snpsIndels/haplotypecaller";
}
my @ugVariants = ();
my @hcVariants = ();
my $ran_ug = 0;
my $ran_hc = 0;
my @ug_jids = ();
my @hc_jids = ();
my $prgj = join(",", @prg_jids);
foreach my $c (@ref_chr){
### NOTE1: GET THIS RANDOM ERROR NOW FOR SNP CALLS
### Unexpectedly couldn't find valid codec for temporary output file
### RERUNNING THE SAME COMMAND SEEMS TO FIX IT
###
### NOTE2: GET SYSTEM MEMORY ISSUE WHEN RUNNING ON THE CLUSTER AND LOTS
### OF INPUT FILES TO UNIFIEDGENOTYPE WITH NUM THREADS > 1 -nt
### NOT A PROBLEM WHEN RUNNING IT WITH LOTS OF INPUT FILES ON RAY
my $irBams2 = join(" ", @{$processedBams{"$c"}});
if($ug){
if(!-e "$output/progress/$pre\_$uID\_$c\_UG.done" || $ran_pr_glob{"$c"}){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$c\_UG", job_hold => "$prgj", cpu => "12", mem => "24", cluster_out => "$output/progress/$pre\_$uID\_$c\_UG.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx24g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R $REF_SEQ --reference_sample_name $species -L $c $multipleTargets --dbsnp $DB_SNP --downsampling_type NONE --annotateNDA --annotation AlleleBalance --annotation AlleleBalanceBySample --annotation HardyWeinberg --genotype_likelihoods_model BOTH --read_filter BadCigar --num_cpu_threads_per_data_thread 12 --out $output/intFiles/$pre\_$c\_UnifiedGenotyper.vcf $irBams2`;
`/bin/touch $output/progress/$pre\_$uID\_$c\_UG.done`;
push @ug_jids, "$pre\_$uID\_$c\_UG";
$ran_ug = 1;
}
}
### NOTE: ANNOTATIONS THAT DON'T WORK:AlleleBalance, HardyWeinberg,IndelType
if(!-e "$output/progress/$pre\_$uID\_$c\_HC.done" || $ran_pr_glob{"$c"}){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_$c\_HC", job_hold => "$prgj", cpu => "30", mem => "90", cluster_out => "$output/progress/$pre\_$uID\_$c\_HC.log");
my $standardParams = Schedule::queuing(%stdParams);
my %addParams = (scheduler => "$scheduler", runtime => "500", priority_project=> "$priority_project", priority_group=> "$priority_group", rerun => "1", iounits => "7");
my $additionalParams = Schedule::additionalParams(%addParams);
my $response = "";
my $HC_submission_num = 0;
while($response !~ /is submitted to default queue/ && $HC_submission_num < 10){
my $time = 60 * $HC_submission_num;
`sleep $time `;
$HC_submission_num++;
my $stamp = localtime(time);
print "$stamp : HC Chromosome $c attempt number $HC_submission_num.\n";
print "Command: $standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx90g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $REF_SEQ -L $c $multipleTargets --dbsnp $DB_SNP --downsampling_type NONE --annotation AlleleBalanceBySample --annotation ClippingRankSumTest --read_filter BadCigar --num_cpu_threads_per_data_thread 30 --out $output/intFiles/$pre\_$c\_HaplotypeCaller.vcf $irBams2\n";
$response = `$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx90g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $REF_SEQ -L $c $multipleTargets --dbsnp $DB_SNP --downsampling_type NONE --annotation AlleleBalanceBySample --annotation ClippingRankSumTest --read_filter BadCigar --num_cpu_threads_per_data_thread 30 --out $output/intFiles/$pre\_$c\_HaplotypeCaller.vcf $irBams2 2>&1`;
print "Response: $response\n";
if($response !~ /is submitted to default queue/ && $HC_submission_num == 10 && $c eq '1'){
`mail -s "HaplotypeCaller Job Not Working" $email <<< "This is an e-mail letting you know that your variants pipeline run for $pre is not submitting HC jobs to the cluster. Please remove all .done files for haplotype caller and rerun the pipeline." `;
}
}
`/bin/touch $output/progress/$pre\_$uID\_$c\_HC.done`;
push @hc_jids, "$pre\_$uID\_$c\_HC";
$ran_hc = 1;
}
push @ugVariants, "--variant $output/intFiles/$pre\_$c\_UnifiedGenotyper.vcf";
push @hcVariants, "--variant $output/intFiles/$pre\_$c\_HaplotypeCaller.vcf";
}
my $hcVars = join(" " , @hcVariants);
my $ran_cv_hc = 0;
my $hcj = join(",", @hc_jids);
my $cvhcj = '';
if(!-e "$output/progress/$pre\_$uID\_CV_HC.done" || $ran_hc){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_CV_HC", job_hold => "$hcj", cpu => "1", mem => "2", cluster_out => "$output/progress/$pre\_$uID\_CV_HC.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T CombineVariants -R $REF_SEQ -o $output/intFiles/$pre\_HaplotypeCaller_RAW.vcf --assumeIdenticalSamples $hcVars`;
`/bin/touch $output/progress/$pre\_$uID\_CV_HC.done`;
$cvhcj = "$pre\_$uID\_CV_HC";
$ran_cv_hc = 1;
}
### NOTE: InbreedingCoeff requires >= 10 samples
### doing a stupid count of just number of unique MD bams that are inputs
### this makes the assumption that there is only 1 MD bam per sample
### which isn't always true e.g. when a sample has multiple libraries
### we treat it as 2 "samples" but gatk will not
my $ran_vr_snp_hc = 0;
my $vrshcj = '';
if(!-e "$output/progress/$pre\_$uID\_VR_SNP_HC.done" || $ran_cv_hc){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_VR_SNP_HC", job_hold => "$cvhcj", cpu => "4", mem => "10", cluster_out => "$output/progress/$pre\_$uID\_VR_SNP_HC.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Xms256m -Xmx10g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T VariantRecalibrator -R $REF_SEQ -input $output/intFiles/$pre\_HaplotypeCaller_RAW.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 $HAPMAP -resource:omni,known=false,training=true,truth=true,prior=12.0 $OMNI_1000G -resource:1000G,known=false,training=true,truth=false,prior=10.0 $PHASE1_SNPS_1000G -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 $DB_SNP -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile $output/intFiles/$pre\_HaplotypeCaller_SNP.recal -tranchesFile $output/intFiles/$pre\_HaplotypeCaller_SNP.tranches -rscriptFile $output/intFiles/$pre\_HaplotypeCaller_SNP.plots.R -nt 4`;
`/bin/touch $output/progress/$pre\_$uID\_VR_SNP_HC.done`;
$vrshcj = "$pre\_$uID\_VR_SNP_HC";
$ran_vr_snp_hc = 1;
}
### NOTE: sometimes throws an error when running with multiple threads
### about not being able to find a tmp file; running with -nt 1 to avoid errors
my $ran_ar_snp_hc = 0;
my $arshcj = '';
if(!-e "$output/progress/$pre\_$uID\_AR_SNP_HC.done" || $ran_vr_snp_hc){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_AR_SNP_HC", job_hold => "$vrshcj", cpu => "1", mem => "1", cluster_out => "$output/progress/$pre\_$uID\_AR_SNP_HC.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T ApplyRecalibration -R $REF_SEQ -input $output/intFiles/$pre\_HaplotypeCaller_RAW.vcf --ts_filter_level 99.0 -mode SNP -tranchesFile $output/intFiles/$pre\_HaplotypeCaller_SNP.tranches -recalFile $output/intFiles/$pre\_HaplotypeCaller_SNP.recal -o $output/intFiles/$pre\_HaplotypeCaller_SNP_vqsr.vcf -nt 1`;
`/bin/touch $output/progress/$pre\_$uID\_AR_SNP_HC.done`;
$arshcj = "$pre\_$uID\_AR_SNP_HC";
$ran_ar_snp_hc = 1;
}
my $ran_vr_indel_hc = 0;
my $vrihcj = '';
if(!-e "$output/progress/$pre\_$uID\_VR_INDEL_HC.done" || $ran_ar_snp_hc){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_VR_INDEL_HC", job_hold => "$arshcj", cpu => "4", mem => "1", cluster_out => "$output/progress/$pre\_$uID\_VR_INDEL_HC.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T VariantRecalibrator -R $REF_SEQ -input $output/intFiles/$pre\_HaplotypeCaller_SNP_vqsr.vcf -resource:mills,known=false,training=true,truth=true,prior=12.0 $MILLS_1000G -an DP -an FS -an MQRankSum -an ReadPosRankSum -mode INDEL -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 --maxGaussians 4 -recalFile $output/intFiles/$pre\_HaplotypeCaller_INDEL.recal -tranchesFile $output/intFiles/$pre\_HaplotypeCaller_INDEL.tranches -rscriptFile $output/intFiles/$pre\_HaplotypeCaller_INDEL.plots.R -nt 4`;
`/bin/touch $output/progress/$pre\_$uID\_VR_INDEL_HC.done`;
$vrihcj = "$pre\_$uID\_VR_INDEL_HC";
$ran_vr_indel_hc = 1;
}
my $ran_ar_indel_hc = 0;
my $arihcj = '';
if(!-e "$output/progress/$pre\_$uID\_AR_INDEL_HC.done" || $ran_vr_indel_hc){
sleep(2);
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_AR_INDEL_HC", job_hold => "$vrihcj", cpu => "1", mem => "1", cluster_out => "$output/progress/$pre\_$uID\_AR_INDEL_HC.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T ApplyRecalibration -R $REF_SEQ -input $output/intFiles/$pre\_HaplotypeCaller_SNP_vqsr.vcf --ts_filter_level 99.0 -mode INDEL -tranchesFile $output/intFiles/$pre\_HaplotypeCaller_INDEL.tranches -recalFile $output/intFiles/$pre\_HaplotypeCaller_INDEL.recal -o $output/variants/snpsIndels/haplotypecaller/$pre\_HaplotypeCaller.vcf -nt 1`;
`/bin/touch $output/progress/$pre\_$uID\_AR_INDEL_HC.done`;
$arihcj = "$pre\_$uID\_AR_INDEL_HC";
$ran_ar_indel_hc = 1;
}
# This runs regardless because it has a .done check in the function
sleep(2);
&generateMaf("$output/variants/snpsIndels/haplotypecaller/$pre\_HaplotypeCaller.vcf", 'HaplotypeCaller', "$arihcj,$ssfj", $ran_ar_indel_hc);
if($ug){
if(!-d "$output/variants/snpsIndels/unifiedgenotyper"){
mkdir("$output/variants/snpsIndels/unifiedgenotyper", 0775) or die "Can't make $output/variants/snpsIndels/unifiedgenotyper";
}
my $ugVars = join(" " , @ugVariants);
my $ran_cv_ug = 0;
my $cvugj = '';
my $ugj = join(",", @ug_jids);
if(!-e "$output/progress/$pre\_$uID\_CV_UG.done" || $ran_ug){
my %stdParams = (scheduler => "$scheduler", job_name => "$pre\_$uID\_CV_UG", job_hold => "$ugj", cpu => "1", mem => "2", cluster_out => "$output/progress/$pre\_$uID\_CV_UG.log");
my $standardParams = Schedule::queuing(%stdParams);
`$standardParams->{submit} $standardParams->{job_name} $standardParams->{job_hold} $standardParams->{cpu} $standardParams->{mem} $standardParams->{cluster_out} $additionalParams $JAVA/java -Djava.io.tmpdir=$tempdir -jar $GATK/GenomeAnalysisTK.jar -T CombineVariants -R $REF_SEQ -o $output/intFiles/$pre\_UnifiedGenotyper_RAW.vcf --assumeIdenticalSamples $ugVars`;
`/bin/touch $output/progress/$pre\_$uID\_CV_UG.done`;