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somaticwrapper.pl
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######### Song Cao###########
##### email: scao@wustl.edu ####
## pipeline for somatic variant callings ##
# somatic_variant_callings.pl #
### updated date: 04/05/2017 ###
### updated date: 04/18/2017 ###
### add vcf2maf.pl ###
### 07/14/2017 ##
##3 vaf_filter.pl ###
### 08/25/2017 ####
### add docker env for mgi ##
### 09/28/17##
## add finishing checks##
### 11/13/17 ###
## add option for log directory##
## 09/26/18 ##
## use mutect1.7; merging using 2 over 3 callers ##
## add tsl for vcf2maf.pl ##
## 08/19/19 ##
## add a checking step for vcf before merging ##
## add smg recovering module, Apr 23, 2020 ##
## cp1 version, Oct 06, 2021
#!/usr/bin/perl
##!/gscmnt/gc2525/dinglab/rmashl/Software/perl/perl-5.22.0/bin/perl
use strict;
use warnings;
#use POSIX;
use Getopt::Long;
my $version = 2.2;
#color code
my $red = "\e[31m";
my $gray = "\e[37m";
my $yellow = "\e[33m";
my $green = "\e[32m";
my $purple = "\e[35m";
my $cyan = "\e[36m";
my $normal = "\e[0m";
#usage information
(my $usage = <<OUT) =~ s/\t+//g;
Somatic variant calling pipeline
Pipeline version: $version
$yellow
Usage: perl $0 --srg --sre --wgs --rdir --ref --log --q --mincovt --mincovn --minvaf --maxindsize --exonic --smg --groupname --users --step
$normal
<rdir> = full path of the folder holding files for this sequence run (user must provide)
<log> = full path of the folder for saving log file; usually upper folder of rdir
<wgs> = 1 if it is wgs data and otherwise it is 0; If you want to output the maf for all variants, set exonic to 0
<groupname> = job group name
<users> = user name for job group
<srg> = bam having read group or not: 1, yes and 0, no (default 1)
<sre> = re-run and overwrite previous results: 1, yes and 0, no (default 0)
>>>>>>> a4a79c27f83ba1ebce51a18020e77b941eb33d2b
<step> run this pipeline step by step. (user must provide)
<ref> the human reference:
<q> which queue for submitting job; research-hpc, ding-lab, long (default)
<mincovt> minimum coverage for tumor: default >=14
<mincovn> minimum coverage for normal: default >=8
<minvaf> minimum somatic vaf: default >=0.05
<maxindsize> default <=100
<exonic> output exonic region: 1 Yes, 0 No
<smg> use smg list for calling
hg38: /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa
$green [1] Run streka
$green [2] Run Varscan
$green [3] Run Pindel
$green [4] Run mutect
$yellow [5] Parse mutect result
$yellow [6] Parse streka result
$yellow [7] Parse VarScan result
$yellow [8] Parse Pindel
$cyan [9] QC vcf files
$cyan [10] Merge vcf files
$cyan [11] Generate maf file
$cyan [12] Generate merged maf file
$cyan [13] Annotate dnp and remove nearby snv near an indel
$red [14] Clean unnecessary intermediate files
$normal
OUT
#__DEFAULT NUMBER OF BINS IE (MUST BE INTEGER)
my $step_number = -1;
my $status_rg = 1;
my $status_rerun=0;
my $status_exonic=1;
#__HELP (BOOLEAN, DEFAULTS TO NO-HELP)
my $help = 0;
my $q_name="";
my $s_wgs="";
#__FILE NAME (STRING, NO DEFAULT)
my $run_dir="";
my $log_dir="";
my $h38_REF="";
my $db_smg="";
#my $ref_name="";
my $chr_status=0;
my $maxindsize=100;
my $mincov_t=14;
my $mincov_n=8;
my $minvaf=0.05;
my $compute_username="";
my $group_name="";
#__PARSE COMMAND LINE
my $status = &GetOptions (
"step=i" => \$step_number,
"srg=i" => \$status_rg,
"sre=i" => \$status_rerun,
"wgs=i" => \$s_wgs,
"groupname=s" => \$group_name,
"users=s" => \$compute_username,
"exonic=i" => \$status_exonic,
"rdir=s" => \$run_dir,
"ref=s" => \$h38_REF,
"smg=s" => \$db_smg,
"log=s" => \$log_dir,
"q=s" => \$q_name,
"mincovt=i" => \$mincov_t,
"mincovn=i" => \$mincov_n,
"minvaf=f" => \$minvaf,
"maxindsize=i" => \$maxindsize,
"log=s" => \$log_dir,
"q=s" => \$q_name,
"help" => \$help,
);
#print $status,"\n";
if ($help || $run_dir eq "" || $log_dir eq "" || $group_name eq "" || $compute_username eq "" || $step_number<0 || $db_smg eq "") {
print "wrong option\n";
print $usage;
exit;
}
print "run dir=",$run_dir,"\n";
print "log dir=",$log_dir,"\n";
print "step num=",$step_number,"\n";
print "status rerun=",$status_rerun,"\n";
print "status exonic=",$status_exonic,"\n";
print "status readgroup=",$status_rg,"\n";
print "queue name=",$q_name,"\n";
print "minvaf = ",$minvaf,"\n";
print "job group=",$group_name,"\n";
print "user group=",$compute_username,"\n";
#<STDIN>;
#exit;
if($q_name eq "")
{
$q_name="long";
}
if($s_wgs eq "")
{
$s_wgs=0;
}
if ($run_dir =~/(.+)\/$/) {
$run_dir = $1;
}
die $usage unless ($step_number >=0)&&(($step_number <= 14));
my $email = "scao\@wustl\.edu";
my $HOME = $ENV{HOME};
my $working_name= (split(/\//,$run_dir))[-1];
my $HOME1=$log_dir;
if (! -d $HOME1)
{
`mkdir $HOME1`;
}
if (! -d $HOME1."/tmpsomatic") {
`mkdir $HOME1"/tmpsomatic"`;
}
my $job_files_dir = $HOME1."/tmpsomatic";
#store SGE output and error files here
if (! -d $HOME1."/LSF_DIR_SOMATIC") {
`mkdir $HOME1"/LSF_DIR_SOMATIC"`;
}
my $lsf_file_dir = $HOME1."/LSF_DIR_SOMATIC";
#GENOMEVIP_SCRIPTS=/gscmnt/gc2525/dinglab/rmashl/Software/bin/genomevip
# obtain script path
#my $script_dir="/gscuser/scao/scripts/git/somaticwrapper";
my $run_script_path =`echo \$PWD`;
chomp $run_script_path;
#my $run_script_path = `dirname $0`;
my $script_dir=$run_script_path;
print $script_dir,"\n";
#<STDIN>;
#my $run_script_path=$script_dir;
#chomp $run_script_path;
#$run_script_path = "/gscmnt/gc2525/dinglab/rmashl/Software/perl/perl-5.22.0/bin/perl ".$run_script_path."/";
$run_script_path = "/usr/bin/perl ".$run_script_path."/";
print $run_script_path,"\n";
my $hold_RM_job = "norm";
my $current_job_file = "";#cannot be empty
my $hold_job_file = "";
my $bsub_com = "";
my $sample_full_path = "";
my $sample_name = "";
### running tools: USER needs to change according where the tools are installed.##
#my $mutect="/gscuser/scao/tools/mutect-1.1.7.jar";
my $STRELKA_DIR2="/storage1/fs1/songcao/Active/Software/strelka-2.9.10.centos6_x86_64/bin";
my $pindel="/storage1/fs1/songcao/Active/Software/anaconda3/bin/pindel";
my $PINDEL_DIR="/storage1/fs1/songcao/Active/Software/anaconda3/bin";
my $picardexe="/storage1/fs1/songcao/Active/Software/picard/picard.jar";
my $gatk="/storage1/fs1/songcao/Active/Software/GenomeAnalysis/GenomeAnalysisTK.jar";
my $java_dir="/storage1/fs1/songcao/Active/Software/jre1.8.0_121";
my $java_mutect="/storage1/fs1/songcao/Active/Software/jre1.7.0_80";
my $snpsift="/storage1/fs1/songcao/Active/Software/snpEff/20150522/SnpSift.jar";
my $gatkexe3="/storage1/fs1/songcao/Active/Software/gatk/3.7/GenomeAnalysisTK.jar";
my $mutect1="/storage1/fs1/songcao/Active/Software/mutect/mutect-1.1.7.jar";
my $samtools="/storage1/fs1/songcao/Active/Software/samtools/1.2/bin";
my $samtoolsexe="/storage1/fs1/songcao/Active/Software/samtools/1.2/bin/samtools";
my $varscan="/storage1/fs1/songcao/Active/Software/varscan/2.3.8.ndown";
my $bamreadcount="/storage1/fs1/songcao/Active/Software/bam-readcount/0.7.4/bam-readcount";
#my $vepannot="/storage1/fs1/songcao/Active/Database/hg38_database/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/variant_effect_predictor.v102.pl";
my $vepannot="/storage1/fs1/dinglab/Active/Projects/scao/gitshared/ensembl-vep/vep";
#my $vepcache="/storage1/fs1/songcao/Active/Database/hg38_database/vep/v85";
my $vepcache="/storage1/fs1/songcao/Active/Database/hg38_database/vep/v102";
my $DB_SNP_NO_CHR="/storage1/fs1/songcao/Active/Database/hg38_database/DBSNP/00-All.vcf";
my $DB_SNP="/storage1/fs1/songcao/Active/Database/hg38_database/DBSNP/00-All.chr.vcf";
my $DB_COSMIC="/storage1/fs1/songcao/Active/Database/hg38_database/cosmic/CosmicAllMuts.HG38.sort.chr.vcf";
my $DB_COSMIC_NO_CHR="/storage1/fs1/songcao/Active/Database/hg38_database/cosmic/CosmicAllMuts.HG38.sort.vcf";
my $DB_SNP_NO_COSMIC="/storage1/fs1/songcao/Active/Database/hg38_database/cosmic/00-All.HG38.pass.cosmic.vcf";
my $f_ref_annot="/storage1/fs1/songcao/Active/Database/hg38_database/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa";
my $TSL_DB="/storage1/fs1/songcao/Active/Database/tsl/wgEncodeGencodeTranscriptionSupportLevelV23.txt";
my $h38_REF_bai=$h38_REF.".fai";
my $f_gtf= "/storage1/fs1/songcao/Active/Database/hg38_database/GTF/Homo_sapiens.GRCh38.85.gtf";
my $first_line=`head -n 1 $h38_REF`;
if($first_line=~/^\>chr/) { $chr_status=1; }
opendir(DH, $run_dir) or die "Cannot open dir $run_dir: $!\n";
my @sample_dir_list = readdir DH;
close DH;
# check to make sure the input directory has correct structure
#&check_input_dir($run_dir);
# start data processsing
#`bgadd -L 70 $compute_username/$group_name`;
if (($step_number < 12 && $step_number>0) || $step_number == 14) {
#begin to process each sample
for (my $i=0;$i<@sample_dir_list;$i++) {#use the for loop instead. the foreach loop has some problem to pass the global variable $sample_name to the sub functions
$sample_name = $sample_dir_list[$i];
if (!($sample_name =~ /\./ || $sample_name=~/worklog/)) {
$sample_full_path = $run_dir."/".$sample_name;
if (-d $sample_full_path) { # is a full path directory containing a sample
print $yellow, "\nSubmitting jobs for the sample ",$sample_name, "...",$normal, "\n";
# sleep 1;
$current_job_file="";
if($step_number==0)
{
&bsub_strelka();
&bsub_varscan();
&bsub_pindel();
&bsub_mutect();
&bsub_parse_mutect();
&bsub_parse_strelka();
&bsub_parse_varscan();
&bsub_parse_pindel();
&bsub_merge_vcf();
&bsub_vcf_2_maf();
}elsif ($step_number == 1) {
&bsub_strelka();
}elsif ($step_number == 2) {
&bsub_varscan(1);
}elsif ($step_number == 3) {
&bsub_pindel(1);
}elsif ($step_number == 4){
&bsub_mutect(1);
}elsif ($step_number == 5){
&bsub_parse_mutect(1);
}elsif ($step_number == 6) {
&bsub_parse_strelka(1);
}elsif ($step_number == 7) {
&bsub_parse_varscan(1);
}elsif ($step_number == 8) {
&bsub_parse_pindel(1);
}elsif ($step_number == 9) {
&bsub_qc_vcf(1);
}elsif ($step_number == 10) {
&bsub_merge_vcf(1);
}elsif ($step_number == 11) {
&bsub_vcf_2_maf(1);
}elsif ($step_number == 14) {
&bsub_clean(1);
}
}
}
}
}
if($step_number==12)
{
print $yellow, "Submitting jobs for generating the report for the run ....",$normal, "\n";
$hold_job_file=$current_job_file;
$current_job_file = "j12_Run_report_".$working_name.".sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
`rm $current_job_file`;
my $working_name= (split(/\//,$run_dir))[-1];
my $f_maf=$run_dir."/".$working_name.".withmutect.maf";
my $f_maf_rc=$f_maf.".rc";
my $f_maf_rc_caller=$f_maf_rc.".caller";
open(REPRUN, ">$job_files_dir/$current_job_file") or die $!;
print REPRUN "#!/bin/bash\n";
print REPRUN " ".$run_script_path."generate_final_report.pl ".$run_dir." ".$status_exonic."\n";
print REPRUN " ".$run_script_path."add_rc.pl ".$run_dir." ".$f_maf." ".$f_maf_rc."\n";
print REPRUN " ".$run_script_path."add_caller.pl ".$run_dir." ".$f_maf_rc." ".$f_maf_rc_caller."\n";
close REPRUN;
my $sh_file=$job_files_dir."/".$current_job_file;
$bsub_com = "bsub -g /$compute_username/$group_name -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n";
print $bsub_com;
system ($bsub_com);
}
### Annotate dnp
### keep indel (for cocoexistence of indel and snv)
print "annotation\n";
if($step_number==13)
{
print $yellow, "annotate dnp and remove snv near an indel",$normal, "\n";
$hold_job_file=$current_job_file;
$current_job_file = "j13_dnp_".$working_name.".sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
#`rm $current_job_file`;
my $working_name= (split(/\//,$run_dir))[-1];
my $f_maf=$run_dir."/".$working_name.".withmutect.maf.rc.caller";
my $f_maf_rm_snv=$run_dir."/".$working_name.".remove.nearby.snv.maf";
my $f_maf_removed=$run_dir."/".$working_name.".remove.nearby.snv.maf.removed";
my $f_maf_dnp_tmp=$run_dir."/".$working_name.".dnp.annotated.tmp.maf";
my $f_maf_dnp_tmp_merge=$run_dir."/".$working_name.".dnp.annotated.tmp.maf.merge";
my $f_maf_dnp=$run_dir."/".$working_name.".dnp.annotated.maf";
my $f_maf_coding_dnp=$run_dir."/".$working_name.".dnp.annotated.coding.maf";
my $f_bam_list=$run_dir."/input.bam.list";
open(OUTB,">$f_bam_list");
foreach my $s (`ls $run_dir`)
{
my $str=$s;
chomp($str);
my $dir_2=$run_dir."/".$str;
if(-d $dir_2)
{
my $f_bam=$dir_2."/".$str.".T.bam";
if(-e $f_bam) { print OUTB $str,"_T","\t",$f_bam,"\n"; }
}
}
open(DNP, ">$job_files_dir/$current_job_file") or die $!;
print DNP "#!/bin/bash\n";
print DNP " ".$run_script_path."remove_nearby_snv.pl $f_maf $f_maf_rm_snv"."\n";
print DNP " ".$run_script_path."cocoon.pl $f_maf_rm_snv $f_maf_dnp_tmp $log_dir --bam $f_bam_list --samt $samtoolsexe --merge --genome $h38_REF --gtf $f_gtf --snvonly"."\n";
print DNP " ".$run_script_path."add_dnp.pl $f_maf_rm_snv $f_maf_dnp_tmp_merge $f_maf_dnp"."\n";
print DNP " ".$run_script_path."generate_coding_report.pl $f_maf_dnp $f_maf_coding_dnp"."\n";
### remove tmp files ##
print DNP "rm $f_maf_dnp_tmp_merge\n";
print DNP "rm $f_maf_dnp_tmp\n";
print DNP "rm $f_maf_rm_snv\n";
print DNP "rm $f_maf_removed\n";
#print DNP " ".$run_script_path."add_caller.pl ".$run_dir." ".$f_maf_rc." ".$f_maf_rc_caller."\n";
close DNP;
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
#system ($bsub_com);
my $sh_file=$job_files_dir."/".$current_job_file;
$bsub_com = "bsub -g /$compute_username/$group_name -q $q_name -n 1 -R \"select[mem>100000] rusage[mem=100000]\" -M 100000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n";
print $bsub_com;
system ($bsub_com);
}
exit;
## run strelka
sub bsub_strelka{
#my $cdhitReport = $sample_full_path."/".$sample_name.".fa.cdhitReport";
$current_job_file = "j1_streka_".$sample_name.".sh";
my $IN_bam_T = $sample_full_path."/".$sample_name.".T.bam";
my $IN_bam_N = $sample_full_path."/".$sample_name.".N.bam";
if (! -e $IN_bam_T) {#make sure there is a input fasta file
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
print "Warning: Died because there is no input bam file for bwa:\n";
print "File $IN_bam_T does not exist!\n";
die "Please check command line argument!", $normal, "\n\n";
}
if (! -s $IN_bam_T) {#make sure input fasta file is not empty
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
die "Warning: Died because $IN_bam_T is empty!", $normal, "\n\n";
}
if (! -e $IN_bam_N) {#make sure there is a input fasta file
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
print "Warning: Died because there is no input bam file for bwa:\n";
print "File $IN_bam_N does not exist!\n";
die "Please check command line argument!", $normal, "\n\n";
}
if (! -s $IN_bam_N) {#make sure input fasta file is not empty
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
die "Warning: Died because $IN_bam_N is empty!", $normal, "\n\n";
}
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
#`rm $current_job_file`;
open(STREKA, ">$job_files_dir/$current_job_file") or die $!;
print STREKA "#!/bin/bash\n";
#print STREKA "#BSUB -n 1\n";
#print STREKA "#BSUB -R \"rusage[mem=30000]\"","\n";
#print STREKA "#BSUB -M 30000000\n";
#print STREKA "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
#print STREKA "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
#print STREKA "#BSUB -J $current_job_file\n";
#print STREKA "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print STREKA "#BSUB -q long\n";
#print STREKA "#BSUB -q research-hpc\n";
#print STREKA "#BSUB -q long\n";
#print STREKA "scr_t0=\`date \+\%s\`\n";
print STREKA "TBAM=".$sample_full_path."/".$sample_name.".T.bam\n";
print STREKA "NBAM=".$sample_full_path."/".$sample_name.".N.bam\n";
print STREKA "myRUNDIR=".$sample_full_path."/strelka\n";
print STREKA "STATUSDIR=".$sample_full_path."/status\n";
print STREKA "RESULTSDIR=".$sample_full_path."/results\n";
print STREKA "SG_DIR=".$sample_full_path."/strelka\n";
print STREKA "RUNDIR=".$sample_full_path."\n";
print STREKA "STRELKA_OUT=".$sample_full_path."/strelka/strelka_out"."\n";
print STREKA "STRELKA_VCF=".$sample_full_path."/strelka/strelka_out/results/somatic.snvs.vcf.gz"."\n";
#print STREKA "STRELKA_VCF=".$sample_full_path."/strelka/strelka_out/results/passed.somatic.snvs.vcf"."\n";
#print STREKA "CONFDIR="."/gscmnt/gc2521/dinglab/cptac_prospective_samples/exome/config\n";
print STREKA "TASK_STATUS=".$sample_full_path."/strelka/strelka_out/task.complete"."\n";
print STREKA "export SAMTOOLS_DIR=$samtools\n";
print STREKA "export JAVA_HOME=$java_dir\n";
print STREKA "export JAVA_OPTS=\"-Xmx10g\"\n";
print STREKA "export PATH=\${JAVA_HOME}/bin:\${PATH}\n";
print STREKA "if [ ! -d \${myRUNDIR} ]\n";
print STREKA "then\n";
print STREKA "mkdir \${myRUNDIR}\n";
print STREKA "fi\n";
### re-run, then delete task.complete file ###
print STREKA "if [ $status_rerun -eq 1 ]\n";
print STREKA " then\n";
print STREKA "rm \${TASK_STATUS}\n";
print STREKA "fi\n";
## if STRELKA_VCF not existed
print STREKA "if [ ! -f \${STRELKA_VCF} ]\n";
print STREKA " then\n";
print STREKA "rm \${TASK_STATUS}\n";
print STREKA "fi\n";
print STREKA "if [ ! -f \${TASK_STATUS} ]\n";
print STREKA "then\n";
print STREKA "if [ -d \${STRELKA_OUT} ]\n";
print STREKA "then\n";
print STREKA "rm -rf \${STRELKA_OUT}\n";
print STREKA "fi\n";
print STREKA "if \[\[ -z \"\$LD_LIBRARY_PATH\" \]\] \; then\n";
print STREKA "export LD_LIBRARY_PATH=\${JAVA_HOME}/lib\n";
print STREKA "else\n";
print STREKA "export LD_LIBRARY_PATH=\${JAVA_HOME}/lib:\${LD_LIBRARY_PATH}\n";
print STREKA "fi\n";
#print STREKA "put_cmd=\"ln -s\"\n";
#print STREKA "del_cmd=\"rm -f\"\n";
#print STREKA "del_local=\"rm -f\"\n";
#print STREKA "statfile=incomplete.strelka\n";
#print STREKA "localstatus=".$sample_full_path."/status/\$statfile\n";
#print STREKA "touch \$localstatus\n";
#print STREKA ". $script_dir/set_envvars\n";
# print STREKA ". /gscmnt/gc2525/dinglab/rmashl/Software/perl/set_envvars\n";
# print STREKA
print STREKA "if [ $s_wgs -eq 1 ]\n";
print STREKA " then\n";
print STREKA " ".$STRELKA_DIR2."/configureStrelkaSomaticWorkflow.py --normalBam=\$NBAM --tumorBam=\$TBAM --referenceFasta=$h38_REF --callMemMb=1024 --runDir=\$STRELKA_OUT\n";
print STREKA "else\n";
print STREKA " ".$STRELKA_DIR2."/configureStrelkaSomaticWorkflow.py --normalBam=\$NBAM --tumorBam=\$TBAM --referenceFasta=$h38_REF --callMemMb=1024 --exome --runDir=\$STRELKA_OUT\n";
#print STREKA " ".$STRELKA_DIR2."/configureStrelkaWorkflow.pl --normal \$NBAM --tumor \$TBAM --ref ". $h38_REF." --config $script_dir/strelka.ini --output-dir \$STRELKA_OUT\n";
print STREKA "fi\n";
print STREKA "cd \$STRELKA_OUT\n";
print STREKA "\$STRELKA_OUT/runWorkflow.py -m local -j 8 -g 4\n";
print STREKA "touch \${TASK_STATUS}\n";
print STREKA "fi\n";
close STREKA;
my $sh_file=$job_files_dir."/".$current_job_file;
if($q_name eq "research-hpc")
{
$bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n"; }
else {
$bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -o $lsf_out -e $lsf_err bash $sh_file\n";
}
#$bsub_com = "LSF_DOCKER_PRESERVE_ENVIRONMENT=false bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n";
$bsub_com = "bsub -g /$compute_username/$group_name -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n";
print $bsub_com;
system ($bsub_com);
}
## run varscan
sub bsub_varscan{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j2_varscan_".$sample_name.".sh";
my $IN_bam_T = $sample_full_path."/".$sample_name.".T.bam";
my $IN_bam_N = $sample_full_path."/".$sample_name.".N.bam";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
if (! -e $IN_bam_T) {#make sure there is a input fasta file
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
print "Warning: Died because there is no input bam file for bwa:\n";
print "File $IN_bam_T does not exist!\n";
die "Please check command line argument!", $normal, "\n\n";
}
if (! -s $IN_bam_T) {#make sure input fasta file is not empty
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
die "Warning: Died because $IN_bam_T is empty!", $normal, "\n\n";
}
if (! -e $IN_bam_N) {#make sure there is a input fasta file
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
print "Warning: Died because there is no input bam file for bwa:\n";
print "File $IN_bam_N does not exist!\n";
die "Please check command line argument!", $normal, "\n\n";
}
if (! -s $IN_bam_N) {#make sure input fasta file is not empty
print $red, "&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n";
die "Warning: Died because $IN_bam_N is empty!", $normal, "\n\n";
}
open(VARSCAN, ">$job_files_dir/$current_job_file") or die $!;
print VARSCAN "#!/bin/bash\n";
# print VARSCAN "#BSUB -n 1\n";
# print VARSCAN "#BSUB -R \"rusage[mem=30000]\"","\n";
# print VARSCAN "#BSUB -M 30000000\n";
# print VARSCAN "#BSUB -o $lsf_file_dir","/","$current_job_file.out\n";
# print VARSCAN "#BSUB -e $lsf_file_dir","/","$current_job_file.err\n";
# print VARSCAN "#BSUB -J $current_job_file\n";
# print VARSCAN "#BSUB -w \"$hold_job_file\"","\n";
# print VARSCAN "#BSUB -q long\n";
#print VARSCAN "#BSUB -a \'docker(registry.gsc.wustl.edu/genome/genome_perl_environment)\'\n";
#print VARSCANP "#BSUB -q long\n";
#print VARSCAN "#BSUB -q research-hpc\n";
print VARSCAN "TBAM=".$sample_full_path."/".$sample_name.".T.bam\n";
print VARSCAN "NBAM=".$sample_full_path."/".$sample_name.".N.bam\n";
print VARSCAN "myRUNDIR=".$sample_full_path."/varscan\n";
print VARSCAN "STATUSDIR=".$sample_full_path."/status\n";
print VARSCAN "RESULTSDIR=".$sample_full_path."/varscan_results\n";
print VARSCAN "RUNDIR=".$sample_full_path."\n";
#print VARSCAN "CONFDIR="."/gscmnt/gc2521/dinglab/cptac_prospective_samples/exome/config\n";
#print VARSCAN "GENOMEVIP_SCRIPTS=/gscmnt/gc2525/dinglab/rmashl/Software/bin/genomevip\n";
print VARSCAN "export VARSCAN_DIR=$varscan\n";
print VARSCAN "export SAMTOOLS_DIR=$samtools\n";
print VARSCAN "export JAVA_HOME=$java_dir\n";
print VARSCAN "export JAVA_OPTS=\"-Xmx10g\"\n";
print VARSCAN "export PATH=\${JAVA_HOME}/bin:\${PATH}\n";
print VARSCAN "if [ ! -d \${myRUNDIR} ]\n";
print VARSCAN "then\n";
print VARSCAN "mkdir \${myRUNDIR}\n";
print VARSCAN "fi\n";
print VARSCAN "if \[\[ -z \"\$LD_LIBRARY_PATH\" \]\] \; then\n";
print VARSCAN "export LD_LIBRARY_PATH=\${JAVA_HOME}/lib\n";
print VARSCAN "else\n";
print VARSCAN "export LD_LIBRARY_PATH=\${JAVA_HOME}/lib:\${LD_LIBRARY_PATH}\n";
print VARSCAN "fi\n";
print VARSCAN "put_cmd=\"ln -s\"\n";
print VARSCAN "del_cmd=\"rm -f\"\n";
print VARSCAN "del_local=\"rm -f\"\n";
print VARSCAN "statfile=complete.vs_som_snvindels\n";
print VARSCAN "localstatus=\${myRUNDIR}\/status\/\${statfile}\n";
print VARSCAN "varscan_vcf=\${myRUNDIR}\/varscan.out.som_snv.vcf\n";
print VARSCAN "if [ ! -d \${myRUNDIR}\/status ]\n";
print VARSCAN "then\n";
print VARSCAN "mkdir \${myRUNDIR}\/status\n";
print VARSCAN "fi\n";
### re-run, then delete complete.vs_som_snvindel file ###
print VARSCAN "if [ $status_rerun -eq 1 ]\n";
print VARSCAN " then\n";
print VARSCAN "rm \${localstatus}\n";
print VARSCAN "fi\n";
# check if vcf file exists
print VARSCAN "if [ ! -f \${varscan_vcf} ]\n";
print VARSCAN " then\n";
print VARSCAN "rm \${localstatus}\n";
print VARSCAN "fi\n";
print VARSCAN "if [ ! -f \${localstatus} ]\n";
print VARSCAN "then\n";
print VARSCAN "cd \${RUNDIR}/varscan\n";
print VARSCAN "TMPBASE=.\/varscan.out.som\n";
print VARSCAN "LOG=\${TMPBASE}.log\n";
print VARSCAN "snvoutbase=\${TMPBASE}_snv\n";
print VARSCAN "indeloutbase=\${TMPBASE}_indel\n";
print VARSCAN "BAMLIST=\${RUNDIR}/varscan/bamfilelist.inp\n";
print VARSCAN "if [ ! -e \${BAMLIST} ]\n";
print VARSCAN "then\n";
print VARSCAN "rm \${BAMLIST}\n";
print VARSCAN "fi\n";
print VARSCAN "echo \"$IN_bam_N\" > \${BAMLIST}\n";
print VARSCAN "echo \"$IN_bam_T\" >> \${BAMLIST}\n";
print VARSCAN "ncols=9\n";
print VARSCAN "\${SAMTOOLS_DIR}/samtools mpileup -q 1 -Q 13 -B -f $h38_REF -b \${BAMLIST} | awk -v ncols=\$ncols \'NF==ncols\' | java \${JAVA_OPTS} -jar \${VARSCAN_DIR}/VarScan.jar somatic - \${TMPBASE} --mpileup 1 --p-value 0.99 --somatic-p-value 0.05 --min-coverage-normal $mincov_n --min-coverage-tumor $mincov_t --min-var-freq $minvaf --min-freq-for-hom 0.75 --normal-purity 1.00 --tumor-purity 1.00 --strand-filter 1 --min-avg-qual 15 --output-vcf 1 --output-snp \${snvoutbase} --output-indel \${indeloutbase} &> \${LOG}\n";
print VARSCAN ' grep "Error occurred during initialization of VM" ${LOG}',"\n";# one possible blast error (see the end of this script).
print VARSCAN ' CHECK=$?',"\n";
print VARSCAN ' while [ ${CHECK} -eq 0 ]',"\n";
print VARSCAN " do\n";
print VARSCAN "\${SAMTOOLS_DIR}/samtools mpileup -q 1 -Q 13 -B -f $h38_REF -b \${BAMLIST} | awk -v ncols=\$ncols \'NF==ncols\' | java \${JAVA_OPTS} -jar \${VARSCAN_DIR}/VarScan.jar somatic - \${TMPBASE} --mpileup 1 --p-value 0.99 --somatic-p-value 0.05 --min-coverage-normal $mincov_n --min-coverage-tumor $mincov_t --min-var-freq $minvaf --min-freq-for-hom 0.75 --normal-purity 1.00 --tumor-purity 1.00 --strand-filter 1 --min-avg-qual 15 --output-vcf 1 --output-snp \${snvoutbase} --output-indel \${indeloutbase} &> \${LOG}\n";
print VARSCAN ' grep "Error occurred during initialization of VM" ${LOG}',"\n";
print VARSCAN ' CHECK=$?',"\n";
print VARSCAN " done\n";
#print VARSCAN " fi\n";
print VARSCAN "touch \${localstatus}\n";
print VARSCAN "fi\n";
close VARSCAN;
my $sh_file=$job_files_dir."/".$current_job_file;
# if($q_name eq "research-hpc")
# {
# $bsub_com = "bsub -q research-hpc -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -w \"$hold_job_file\" -o $lsf_out -e $lsf_err bash $sh_file\n"; }
# else { $bsub_com = "bsub -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -w \"$hold_job_file\" -o $lsf_out -e $lsf_err bash $sh_file\n"; }
# print $bsub_com;
# system ($bsub_com);
$bsub_com = "LSF_DOCKER_PRESERVE_ENVIRONMENT=false bsub -g /$compute_username/$group_name -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n";
print $bsub_com;
system ($bsub_com);
#$bsub_com = "bsub < $job_files_dir/$current_job_file\n";
#system ( $bsub_com );
}
sub bsub_parse_strelka{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j6_parse_strelka".$sample_name.".sh";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
my $IN_bam_T = $sample_full_path."/".$sample_name.".T.bam";
my $IN_bam_N = $sample_full_path."/".$sample_name.".N.bam";
open(STREKAP, ">$job_files_dir/$current_job_file") or die $!;
print STREKAP "#!/bin/bash\n";
print STREKAP "TBAM=".$sample_full_path."/".$sample_name.".T.bam\n";
print STREKAP "NBAM=".$sample_full_path."/".$sample_name.".N.bam\n";
print STREKAP "myRUNDIR=".$sample_full_path."/strelka\n";
print STREKAP "STATUSDIR=".$sample_full_path."/status\n";
print STREKAP "RESULTSDIR=".$sample_full_path."/results\n";
print STREKAP "SG_DIR=".$sample_full_path."/strelka\n";
print STREKAP "RUNDIR=".$sample_full_path."\n";
print STREKAP "STRELKA_OUT=".$sample_full_path."/strelka/strelka_out"."\n";
print STREKAP "export SAMTOOLS_DIR=$samtools\n";
print STREKAP "export VARSCAN_DIR=$varscan\n";
print STREKAP "export JAVA_HOME=$java_dir\n";
print STREKAP "export JAVA_OPTS=\"-Xmx10g\"\n";
print STREKAP "export PATH=\${JAVA_HOME}/bin:\${PATH}\n";
print STREKAP "cat > \${myRUNDIR}/strelka_out/results/strelka_dbsnp_filter.snv.input <<EOF\n";
print STREKAP "streka.dbsnp.snv.annotator = $snpsift\n";
print STREKAP "streka.dbsnp.snv.db = $DB_SNP_NO_COSMIC\n";
print STREKAP "streka.dbsnp.snv.rawvcf = ./strelka.somatic.snv.strlk_pass.gvip.vcf\n";
print STREKAP "streka.dbsnp.snv.mode = filter\n";
print STREKAP "streka.dbsnp.snv.passfile = ./strelka.somatic.snv.all.gvip.dbsnp_pass.vcf\n";
print STREKAP "streka.dbsnp.snv.dbsnpfile = ./strelka.somatic.snv.all.gvip.dbsnp_present.vcf\n";
print STREKAP "EOF\n";
print STREKAP "cat > \${myRUNDIR}/strelka_out/results/strelka_dbsnp_filter.indel.input <<EOF\n";
print STREKAP "streka.dbsnp.indel.annotator = $snpsift\n";
print STREKAP "streka.dbsnp.indel.db = $DB_SNP_NO_COSMIC\n";
print STREKAP "streka.dbsnp.indel.rawvcf = ./strelka.somatic.indel.strlk_pass.gvip.vcf\n";
print STREKAP "streka.dbsnp.indel.mode = filter\n";
print STREKAP "streka.dbsnp.indel.passfile = ./strelka.somatic.indel.all.gvip.dbsnp_pass.vcf\n";
print STREKAP "streka.dbsnp.indel.dbsnpfile = ./strelka.somatic.indel.all.gvip.dbsnp_present.vcf\n";
print STREKAP "EOF\n";
print STREKAP "FP_BAM=\`awk \'{if(NR==1){print \$1}}\' \${RUNDIR}/varscan/bamfilelist.inp\`\n";
print STREKAP "cat > \${RUNDIR}/strelka/strelka_out/results/strelka_fpfilter.snv.input <<EOF\n";
print STREKAP "strelka.fpfilter.snv.bam_readcount = $bamreadcount\n";
print STREKAP "strelka.fpfilter.snv.bam_file = $IN_bam_T\n";
print STREKAP "strelka.fpfilter.snv.REF = $h38_REF\n";
print STREKAP "strelka.fpfilter.snv.variants_file = \${RUNDIR}/strelka/strelka_out/results/strelka.somatic.snv.all.gvip.dbsnp_pass.vcf\n";
print STREKAP "strelka.fpfilter.snv.passfile = \${RUNDIR}/strelka/strelka_out/results/strelka.somatic.snv.all.gvip.dbsnp_pass.fp_pass.vcf\n";
print STREKAP "strelka.fpfilter.snv.failfile = \${RUNDIR}/strelka/strelka_out/results/strelka.somatic.snv.all.gvip.dbsnp_pass.fp_fail.vcf\n";
print STREKAP "strelka.fpfilter.snv.rc_in = \${RUNDIR}/strelka/strelka_out/results/strelka.somatic.snv.all.gvip.dbsnp_pass.rc.in.vcf\n";
print STREKAP "strelka.fpfilter.snv.rc_out = \${RUNDIR}/strelka/strelka_out/results/strelka.somatic.snv.all.gvip.dbsnp_pass.rc.out.vcf\n";
print STREKAP "strelka.fpfilter.snv.fp_out = \${RUNDIR}/strelka/strelka_out/results/strelka.somatic.snv.all.gvip.dbsnp_pass.fp.out.vcf\n";
print STREKAP "strelka.fpfilter.snv.min_mapping_qual = 0\n";
print STREKAP "strelka.fpfilter.snv.min_base_qual = 15\n";
print STREKAP "strelka.fpfilter.snv.min_num_var_supporting_reads = 4\n";
print STREKAP "strelka.fpfilter.snv.min_var_allele_freq = $minvaf\n";
print STREKAP "strelka.fpfilter.snv.min_avg_rel_read_position = 0.10\n";
print STREKAP "strelka.fpfilter.snv.min_avg_rel_dist_to_3prime_end = 0.10\n";
print STREKAP "strelka.fpfilter.snv.min_var_strandedness = 0.01\n";
print STREKAP "strelka.fpfilter.snv.min_allele_depth_for_testing_strandedness = 5\n";
print STREKAP "strelka.fpfilter.snv.min_ref_allele_avg_base_qual = 30\n";
print STREKAP "strelka.fpfilter.snv.min_var_allele_avg_base_qual = 30\n";
print STREKAP "strelka.fpfilter.snv.max_rel_read_length_difference = 0.25\n";
print STREKAP "strelka.fpfilter.snv.max_mismatch_qual_sum_for_var_reads = 150\n";
print STREKAP "strelka.fpfilter.snv.max_avg_mismatch_qual_sum_difference = 150\n";
print STREKAP "strelka.fpfilter.snv.min_ref_allele_avg_mapping_qual = 30\n";
print STREKAP "strelka.fpfilter.snv.min_var_allele_avg_mapping_qual = 30\n";
print STREKAP "strelka.fpfilter.snv.max_avg_mapping_qual_difference = 50\n";
print STREKAP "EOF\n";
print STREKAP "cd \${STRELKA_OUT}/results\n";
print STREKAP " ".$run_script_path."get_strelka_passed_snv_indel.pl ./variants/somatic.snvs.vcf.gz ./variants/somatic.indels.vcf.gz ./passed.somatic.snvs.vcf ./passed.somatic.indels.vcf\n";
print STREKAP " ".$run_script_path."genomevip_label.pl Strelka ./passed.somatic.snvs.vcf ./strelka.somatic.snv.strlk_pass.gvip.vcf\n";
print STREKAP " ".$run_script_path."genomevip_label.pl Strelka ./passed.somatic.indels.vcf ./strelka.somatic.indel.strlk_pass.gvip.vcf\n";
print STREKAP "strekasnvout=\${STRELKA_OUT}/results/strelka.somatic.snv.all.gvip.dbsnp_pass.vcf\n";
print STREKAP "strekaindelout=\${STRELKA_OUT}/results/strelka.somatic.indel.all.gvip.dbsnp_pass.vcf\n";
print STREKAP "statfile=complete.streka_parser\n";
print STREKAP "localstatus=\${STRELKA_OUT}\/\${statfile}\n";
print STREKAP "if [ $status_rerun -eq 1 ]\n";
print STREKAP " then\n";
print STREKAP "rm \${localstatus}\n";
print STREKAP "fi\n";
print STREKAP "if [ ! -f \${localstatus} ]\n";
print STREKAP "then\n";
print STREKAP " ".$run_script_path."dbsnp_filter.pl ./strelka_dbsnp_filter.snv.input\n";
print STREKAP " ".$run_script_path."dbsnp_filter.pl ./strelka_dbsnp_filter.indel.input\n";
print STREKAP " ".$run_script_path."snv_filter.pl ./strelka_fpfilter.snv.input\n";
print STREKAP ' grep "Error occurred during initialization of VM" ${strekasnvout}',"\n";
print STREKAP ' CHECK=$?',"\n";
print STREKAP ' while [ ${CHECK} -eq 0 ]',"\n";
print STREKAP " do\n";
print STREKAP " ".$run_script_path."dbsnp_filter.pl ./strelka_dbsnp_filter.snv.input\n";
print STREKAP " ".$run_script_path."dbsnp_filter.pl ./strelka_dbsnp_filter.indel.input\n";
print STREKAP " ".$run_script_path."snv_filter.pl ./strelka_fpfilter.snv.input\n";
print STREKAP ' grep "Error occurred during initialization of VM" ${strekasnvout}',"\n";
print STREKAP ' CHECK=$?',"\n";
print STREKAP " done\n";
print STREKAP "touch \${localstatus}\n";
print STREKAP " fi\n";
close STREKAP;
#my $sh_file=$job_files_dir."/".$current_job_file;
my $sh_file=$job_files_dir."/".$current_job_file;
# $bsub_com = "bsub -g /$compute_username/$group_name -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n";
$bsub_com = "bsub -g /$compute_username/$group_name -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n";
print $bsub_com;
system ($bsub_com);
}
sub bsub_parse_varscan{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j7_parse_varscan".$sample_name.".sh";
my $IN_bam_T = $sample_full_path."/".$sample_name.".T.bam";
my $IN_bam_N = $sample_full_path."/".$sample_name.".N.bam";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(VARSCANP, ">$job_files_dir/$current_job_file") or die $!;
print VARSCANP "#!/bin/bash\n";
print VARSCANP "scr_t0=\`date \+\%s\`\n";
print VARSCANP "TBAM=".$sample_full_path."/".$sample_name.".T.bam\n";
print VARSCANP "NBAM=".$sample_full_path."/".$sample_name.".N.bam\n";
print VARSCANP "myRUNDIR=".$sample_full_path."/varscan\n";
print VARSCANP "STATUSDIR=".$sample_full_path."/status\n";
print VARSCANP "RUNDIR=".$sample_full_path."\n";
print VARSCANP "export VARSCAN_DIR=$varscan\n";
print VARSCANP "export SAMTOOLS_DIR=$samtools\n";
print VARSCANP "export JAVA_HOME=$java_dir\n";
print VARSCANP "export JAVA_OPTS=\"-Xmx10g\"\n";
print VARSCANP "export PATH=\${JAVA_HOME}/bin:\${PATH}\n";
print VARSCANP "cat > \${RUNDIR}/varscan/vs_dbsnp_filter.snv.input <<EOF\n";
print VARSCANP "varscan.dbsnp.snv.annotator = $snpsift\n";
print VARSCANP "varscan.dbsnp.snv.db = $DB_SNP_NO_COSMIC\n";
print VARSCANP "varscan.dbsnp.snv.rawvcf = ./varscan.out.som_snv.gvip.Somatic.hc.somfilter_pass.vcf\n";
print VARSCANP "varscan.dbsnp.snv.mode = filter\n";
print VARSCANP "varscan.dbsnp.snv.passfile = ./varscan.out.som_snv.gvip.Somatic.hc.somfilter_pass.dbsnp_pass.vcf\n";
print VARSCANP "varscan.dbsnp.snv.dbsnpfile = ./varscan.out.som_snv.gvip.Somatic.hc.somfilter_pass.dbsnp_present.vcf\n";
print VARSCANP "EOF\n";
print VARSCANP "cat > \${RUNDIR}/varscan/vs_dbsnp_filter.indel.input <<EOF\n";
print VARSCANP "varscan.dbsnp.indel.annotator = $snpsift\n";
print VARSCANP "varscan.dbsnp.indel.db = $DB_SNP_NO_COSMIC\n";
print VARSCANP "varscan.dbsnp.indel.rawvcf = ./varscan.out.som_indel.gvip.Somatic.hc.vcf\n";
print VARSCANP "varscan.dbsnp.indel.mode = filter\n";
print VARSCANP "varscan.dbsnp.indel.passfile = ./varscan.out.som_indel.gvip.Somatic.hc.dbsnp_pass.vcf\n";
print VARSCANP "varscan.dbsnp.indel.dbsnpfile = ./varscan.out.som_indel.gvip.Somatic.hc.dbsnp_present.vcf\n";
print VARSCANP "EOF\n";
print VARSCANP "FP_BAM=\`awk \'{if(NR==2){print \$1}}\' \${RUNDIR}/varscan/bamfilelist.inp\`\n";
print VARSCANP "cat > \${RUNDIR}/varscan/vs_fpfilter.somatic.snv.input <<EOF\n";
print VARSCANP "varscan.fpfilter.snv.bam_readcount = $bamreadcount\n";
print VARSCANP "varscan.fpfilter.snv.bam_file = \${FP_BAM}\n";
print VARSCANP "varscan.fpfilter.snv.REF = $h38_REF\n";
print VARSCANP "varscan.fpfilter.snv.variants_file = ./varscan.out.som_snv.gvip.Somatic.hc.somfilter_pass.dbsnp_pass.vcf\n";
print VARSCANP "varscan.fpfilter.snv.passfile = ./varscan.out.som_snv.gvip.Somatic.hc.somfilter_pass.dbsnp_pass.fp_pass.vcf\n";
print VARSCANP "varscan.fpfilter.snv.failfile = ./varscan.out.som_snv.gvip.Somatic.hc.somfilter_pass.dbsnp_pass.fp_fail.vcf\n";
print VARSCANP "varscan.fpfilter.snv.min_mapping_qual = 0\n";
print VARSCANP "varscan.fpfilter.snv.min_base_qual = 15\n";
print VARSCANP "varscan.fpfilter.snv.min_num_var_supporting_reads = 4\n";
print VARSCANP "varscan.fpfilter.snv.min_var_allele_freq = $minvaf\n";
print VARSCANP "varscan.fpfilter.snv.min_avg_rel_read_position = 0.10\n";
print VARSCANP "varscan.fpfilter.snv.min_avg_rel_dist_to_3prime_end = 0.10\n";
print VARSCANP "varscan.fpfilter.snv.min_var_strandedness = 0.01\n";
print VARSCANP "varscan.fpfilter.snv.min_allele_depth_for_testing_strandedness = 5\n";
print VARSCANP "varscan.fpfilter.snv.min_ref_allele_avg_base_qual = 30\n";
print VARSCANP "varscan.fpfilter.snv.min_var_allele_avg_base_qual = 30\n";
print VARSCANP "varscan.fpfilter.snv.max_rel_read_length_difference = 0.25\n";
print VARSCANP "varscan.fpfilter.snv.max_mismatch_qual_sum_for_var_reads = 150\n";
print VARSCANP "varscan.fpfilter.snv.max_avg_mismatch_qual_sum_difference = 100\n";
print VARSCANP "varscan.fpfilter.snv.min_ref_allele_avg_mapping_qual = 30\n";
print VARSCANP "varscan.fpfilter.snv.min_var_allele_avg_mapping_qual = 30\n";
print VARSCANP "varscan.fpfilter.snv.max_avg_mapping_qual_difference = 50\n";
print VARSCANP "EOF\n";
print VARSCANP "if [ ! -d \${myRUNDIR} ]\n";
print VARSCANP "then\n";
print VARSCANP "mkdir \${myRUNDIR}\n";
print VARSCANP "fi\n";
print VARSCANP "if \[\[ -z \"\$LD_LIBRARY_PATH\" \]\] \; then\n";
print VARSCANP "export LD_LIBRARY_PATH=\${JAVA_HOME}/lib\n";
print VARSCANP "else\n";
print VARSCANP "export LD_LIBRARY_PATH=\${JAVA_HOME}/lib:\${LD_LIBRARY_PATH}\n";
print VARSCANP "fi\n";
print VARSCANP "put_cmd=\"ln -s\"\n";
print VARSCANP "del_cmd=\"rm -f\"\n";
print VARSCANP "del_local=\"rm -f\"\n";
print VARSCANP "statfile=complete.vs_som_parser\n";
print VARSCANP "localstatus=\${myRUNDIR}\/status\/\${statfile}\n";
print VARSCANP "if [ ! -d \${myRUNDIR}\/status ]\n";
print VARSCANP "then\n";
print VARSCANP "mkdir \${myRUNDIR}\/status\n";
print VARSCANP "fi\n";
print VARSCANP "if [ $status_rerun -eq 1 ]\n";
print VARSCANP " then\n";
print VARSCANP "rm \${localstatus}\n";
print VARSCANP "fi\n";
print VARSCANP "if [ ! -f \${localstatus} ]\n";
print VARSCANP "then\n";
print VARSCANP "cd \${RUNDIR}/varscan\n";
print VARSCANP "TMPBASE=.\/varscan.out.som\n";
print VARSCANP "LOG=\${TMPBASE}.log\n";
print VARSCANP "snvoutbase=\${TMPBASE}_snv\n";
print VARSCANP "indeloutbase=\${TMPBASE}_indel\n";
print VARSCANP "cd \${RUNDIR}/varscan\n";
print VARSCANP "if [ ! -f \${snvoutbase}.vcf ]","\n";
print VARSCANP " then\n";
print VARSCANP "mv \${snvoutbase} \${snvoutbase}.vcf","\n";
print VARSCANP "fi\n";
print VARSCANP "if [ ! -f \${indeloutbase}.vcf ]","\n";
print VARSCANP " then\n";
print VARSCANP "mv \${indeloutbase} \${indeloutbase}.vcf","\n";
print VARSCANP "fi\n";
print VARSCANP " ".$run_script_path."genomevip_label.pl VarScan \${snvoutbase}.vcf \${snvoutbase}.gvip.vcf\n";
print VARSCANP " ".$run_script_path."genomevip_label.pl VarScan \${indeloutbase}.vcf \${indeloutbase}.gvip.vcf\n";
print VARSCANP "echo \'APPLYING PROCESS FILTER TO SOMATIC SNVS:\' &>> \${LOG}\n";
print VARSCANP "mysnvorig=./\${snvoutbase}.gvip.vcf\n";
print VARSCANP "java \${JAVA_OPTS} -jar \${VARSCAN_DIR}/VarScan.jar processSomatic \${mysnvorig} --min-tumor-freq $minvaf --max-normal-freq 0.05 --p-value 0.05 &>> \${LOG}\n";
print VARSCANP " ".$run_script_path."extract_somatic_other.pl < \${mysnvorig} > \${mysnvorig/%vcf/other.vcf}\n";
print VARSCANP "for kk in Somatic Germline LOH ; do\n";
print VARSCANP "thisorig=\${mysnvorig/%vcf/\$kk.vcf}\n";
print VARSCANP "thispass=\${mysnvorig/%vcf/\$kk.hc.vcf}\n";
print VARSCANP "thisfail=\${mysnvorig/%vcf/\$kk.lc.vcf}\n";
print VARSCANP "done\n";
print VARSCANP "echo \'APPLYING PROCESS FILTER TO SOMATIC INDELS:\' &>> \$LOG\n";
print VARSCANP "myindelorig=./\$indeloutbase.gvip.vcf\n";
print VARSCANP "java \${JAVA_OPTS} -jar \${VARSCAN_DIR}/VarScan.jar processSomatic \${myindelorig} --min-tumor-freq $minvaf --max-normal-freq 0.05 --p-value 0.05 &>> \${LOG}\n";
print VARSCANP " ".$run_script_path."extract_somatic_other.pl < \${myindelorig} > \${myindelorig/%vcf/other.vcf}\n";
print VARSCANP "for kk in Somatic Germline LOH ; do\n";
print VARSCANP "thisorig=\${myindelorig/%vcf/\$kk.vcf}\n";
print VARSCANP "thispass=\${myindelorig/%vcf/\$kk.hc.vcf}\n";
print VARSCANP "thisfail=\${myindelorig/%vcf/\$kk.lc.vcf}\n";
print VARSCANP "done\n";
print VARSCANP "echo \'APPLYING SOMATIC FILTER:\' &>> \${LOG}\n";
print VARSCANP "thissnvorig=\${snvoutbase}.gvip.Somatic.hc.vcf\n";
print VARSCANP "myindelorig=\${indeloutbase}.gvip.vcf\n";
print VARSCANP "thissnvpass=\${snvoutbase}.gvip.Somatic.hc.somfilter_pass.vcf\n";
print VARSCANP "thissnvfail=\${snvoutbase}.gvip.Somatic.hc.somfilter_fail.vcf\n";
### remove mincov cut-off ##
print VARSCANP "java \${JAVA_OPTS} -jar \${VARSCAN_DIR}/VarScan.jar somaticFilter ./\${thissnvorig} --min-reads2 4 --min-strands2 1 --min-avg-qual 20 --min-var-freq $minvaf --p-value 0.05 --indel-file ./\${myindelorig} --output-file ./\${thissnvpass} &>> \${LOG}\n";
print VARSCANP " ".$run_script_path."dbsnp_filter.pl \${RUNDIR}/varscan/vs_dbsnp_filter.snv.input\n";
print VARSCANP " ".$run_script_path."dbsnp_filter.pl \${RUNDIR}/varscan/vs_dbsnp_filter.indel.input\n";
print VARSCANP "touch \${localstatus}\n";
print VARSCANP "fi\n";
close VARSCANP;
my $sh_file=$job_files_dir."/".$current_job_file;
$bsub_com = "LSF_DOCKER_PRESERVE_ENVIRONMENT=false bsub -g /$compute_username/$group_name -q $q_name -n 1 -R \"select[mem>30000] rusage[mem=30000]\" -M 30000000 -a \'docker(scao/dailybox)\' -o $lsf_out -e $lsf_err bash $sh_file\n";
print $bsub_com;
system ($bsub_com);
}
sub bsub_pindel{
my ($step_by_step) = @_;
if ($step_by_step) {
$hold_job_file = "";
}else{
$hold_job_file = $current_job_file;
}
$current_job_file = "j3_pindel".$sample_name.".sh";
my $IN_bam_T = $sample_full_path."/".$sample_name.".T.bam";
my $IN_bam_N = $sample_full_path."/".$sample_name.".N.bam";
my $lsf_out=$lsf_file_dir."/".$current_job_file.".out";
my $lsf_err=$lsf_file_dir."/".$current_job_file.".err";
`rm $lsf_out`;
`rm $lsf_err`;
open(PINDEL, ">$job_files_dir/$current_job_file") or die $!;
print PINDEL "#!/bin/bash\n";
print PINDEL "TBAM=".$sample_full_path."/".$sample_name.".T.bam\n";
print PINDEL "NBAM=".$sample_full_path."/".$sample_name.".N.bam\n";
print PINDEL "myRUNDIR=".$sample_full_path."/pindel\n";
print PINDEL "CONFIG=\${myRUNDIR}"."/".$sample_name.".config\n";