adding info

alignment/dnaseqalign.sh

@@ -56,9 +56,10 @@ then
 elif [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
 then
     k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p tmphla ${index_path}/genome.fa.alt out.sam| samtools view -1 - > output.unsort.bam
-elif [[ $umi == 'umi' ]] 
+elif [[ $umi == 'umi' ]]
+then
     python ${baseDir}/add_umi_sam.py -s out.sam -o output.unsort.bam
-else 
+else
     samtools view -1 -o output.unsort.bam out.sam
 fi
 which samtools

variants/addgt_virmid.pl

@@ -4,6 +4,10 @@
 my $vcf = shift @ARGV;
 my $out = $vcf;
 $out =~ s/\.vcf/.gt.vcf/g;
+my @headerlines = (qq{##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">},
+		   qq{##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">},
+		   qq{##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">},qq{##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">},
+		   qq{##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">});
 
 open VCF, "<$vcf" or die $!;
 open OUT, ">$out" or die $!;
@@ -11,6 +15,7 @@ while (my $line = <VCF>) {
     chomp($line);
     $line =~ s/ID:/ID=/g;
     if ($line =~ m/#CHROM/) {
+	print OUT join("\n",@headerlines),"\n";
 	print OUT join("\t",$line,'FORMAT','NORMAL','TUMOR'),"\n";
     }elsif ($line =~ m/#/) {
 	print OUT $line,"\n";

variants/somatic_vc.sh

@@ -135,9 +135,10 @@ fi
 
 if [ $algo == 'shimmer' ]
 then
-    module load snpeff/4.3q shimmer/0.1.1 samtools/1.6  vcftools/0.1.14
+    module load shimmer/0.1.1 samtools/1.6  vcftools/0.1.14
     shimmer.pl --minqual 25 --ref ${reffa} ${normal} ${tumor} --outdir shimmer 2> shimmer.err
     perl $baseDir/add_readct_shimmer.pl
+    module load snpeff/4.3q
     vcf-annotate -n --fill-type shimmer/somatic_diffs.readct.vcf | java -jar $SNPEFF_HOME/SnpSift.jar filter '(GEN[*].DP >= 10)' | perl -pe "s/TUMOR/${tid}/" | perl -pe "s/NORMAL/${nid}/g" | bgzip > ${pair_id}.shimmer.vcf.gz
 fi