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Commit 23f16ee

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author
Cao
committed
able to generate two maf (coding and all variant), test pass
1 parent 67a7a28 commit 23f16ee

6 files changed

+93
-12
lines changed

‎generate_coding_report.pl

+42
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,42 @@
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#!/usr/bin/perl
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### for example,
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use strict;
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use warnings;
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die unless @ARGV == 2;
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my ($f_in, $f_out)=@ARGV;
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open(OUT,">$f_out");
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my %count_v;
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my $f_status=$f_out.".status\n";
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open(OUT1,">$f_status");
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foreach my $l (`cat $f_in`)
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{
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my $ltr=$l;
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chomp($ltr);
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if($ltr=~/^#version/) { next; }
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else {
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if($ltr=~/^Hugo/) { print OUT $ltr,"\n"; next; }
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else {
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my @temp=split("\t",$ltr);
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my $annot=$temp[8];
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my $sn=$temp[15];
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$sn=~s/_T//g;
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if($annot=~/Frame_Shift_Del/ || $annot=~/Frame_Shift_Ins/ || $annot=~/Missense_Mutation/ || $annot=~/Nonsense_Mutation/ || $annot=~/Nonstop_Mutation/ || $annot=~/Silent/ || $annot=~/Splice_Site/ || $annot=~/In_Frame_Ins/ || $annot=~/In_Frame_Del/) {
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print OUT $ltr,"\n";
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$count_v{$sn}++;
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}
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}
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}
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}
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close OUT;
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foreach my $s (sort keys %count_v)
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{
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print OUT1 $s,"\t",$count_v{$s},"\n";
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}
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close OUT1;

‎generate_final_report.pl

+3-1
Original file line numberDiff line numberDiff line change
@@ -38,9 +38,11 @@
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my @temp=split("\t",$ltr);
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my $annot=$temp[8];
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my $af=$temp[99];
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if($annot=~/Frame_Shift_Del/ || $annot=~/Frame_Shift_Ins/ || $annot=~/Missense_Mutation/ || $annot=~/Nonsense_Mutation/ || $annot=~/Nonstop_Mutation/ || $annot=~/Silent/ || $annot=~/Splice_Site/ || $annot=~/In_Frame_Ins/ || $annot=~/In_Frame_Del/ || $s_exonic==0) {
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#if($annot=~/Frame_Shift_Del/ || $annot=~/Frame_Shift_Ins/ || $annot=~/Missense_Mutation/ || $annot=~/Nonsense_Mutation/ || $annot=~/Nonstop_Mutation/ || $annot=~/Silent/ || $annot=~/Splice_Site/ || $annot=~/In_Frame_Ins/ || $annot=~/In_Frame_Del/ || $s_exonic==0) {
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#if($af eq "" || (($af ne "") && $af<0.005))
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#{
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if(1==1)
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{
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print OUT1 $ltr,"\n";
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$count++;
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#}

‎somaticwrapper.pl

+12-11
Original file line numberDiff line numberDiff line change
@@ -369,14 +369,15 @@
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my $working_name= (split(/\//,$run_dir))[-1];
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my $f_maf=$run_dir."/".$working_name.".withmutect.maf.rc.caller";
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my $f_maf_rm_snv=$run_dir."/".$working_name.".remove.nearby.snv.maf";
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my $f_maf_removed=$run_dir."/".$working_name.".remove.nearby.snv.maf.removed";
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my $f_maf_dnp_tmp=$run_dir."/".$working_name.".dnp.annotated.tmp.maf";
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my $f_maf_dnp_tmp_merge=$run_dir."/".$working_name.".dnp.annotated.tmp.maf.merge";
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my $f_maf_dnp=$run_dir."/".$working_name.".dnp.annotated.maf";
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my $f_maf_removed=$run_dir."/".$working_name.".remove.nearby.snv.maf.removed";
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my $f_maf_dnp_tmp=$run_dir."/".$working_name.".dnp.annotated.tmp.maf";
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my $f_maf_dnp_tmp_merge=$run_dir."/".$working_name.".dnp.annotated.tmp.maf.merge";
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my $f_maf_dnp=$run_dir."/".$working_name.".dnp.annotated.maf";
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my $f_maf_coding_dnp=$run_dir."/".$working_name.".dnp.annotated.coding.maf";
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my $f_bam_list=$run_dir."/input.bam.list";
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my $f_bam_list=$run_dir."/input.bam.list";
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open(OUTB,">$f_bam_list");
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open(OUTB,">$f_bam_list");
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381382
foreach my $s (`ls $run_dir`)
382383
{
@@ -397,13 +398,13 @@
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}
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399400
open(DNP, ">$job_files_dir/$current_job_file") or die $!;
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400402
print DNP "#!/bin/bash\n";
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## remove snv nearby an indel ##
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print DNP " ".$run_script_path."remove_nearby_snv.pl $f_maf $f_maf_rm_snv"."\n";
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## annotate dnp ##
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print DNP " ".$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 $f_gtf --snvonly"."\n";
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## add dnp to the maf ##
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print DNP " ".$run_script_path."add_dnp.pl $f_maf_rm_snv $f_maf_dnp_tmp_merge $f_maf_dnp"."\n";
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print DNP " ".$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 $f_gtf --snvonly"."\n";
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print DNP " ".$run_script_path."add_dnp.pl $f_maf_rm_snv $f_maf_dnp_tmp_merge $f_maf_dnp"."\n";
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print DNP " ".$run_script_path."generate_coding_report.pl $f_maf_dnp $f_maf_coding_dnp"."\n";
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### remove tmp files ##
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print DNP "rm $f_maf_dnp_tmp_merge\n";
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print DNP "rm $f_maf_dnp_tmp\n";

‎work_log_run_mild

+2
Original file line numberDiff line numberDiff line change
@@ -24,4 +24,6 @@ perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 --sre 1
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perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mild --log /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 12 --sre 1
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perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mild --log /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 13 --sre 1

‎work_log_run_mild_v102

+2
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@@ -4,4 +4,6 @@ perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildvep102 --log /sc
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildvep102 --log /scratch1/fs1/dinglab/scao/sw/mildvep102.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 --sre 1
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perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mildvep102 --log /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mildvep102.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 12 --sre 1
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perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mildvep102 --log /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mildvep102.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 --sre 1

‎work_log_run_pecgsb1

+32
Original file line numberDiff line numberDiff line change
@@ -22,3 +22,35 @@ perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 9
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 10
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 10
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 10
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 11
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 11
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 11
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 12
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 12
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 12
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MM.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.mm.tsv --users songcao --groupname SomaticWXS --step 13
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CHOL.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.chol.tsv --users songcao --groupname SomaticWXS --step 13
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/CRC.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 13
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 1 --sre 1
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 2 --sre 1
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 3 --sre 1
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perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2 --log /scratch1/fs1/dinglab/scao/sw/pecgsb1/MMfail2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.pecgs.crc.tsv --users songcao --groupname SomaticWXS --step 4 --sre 1
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