update shimmer; update filter to not remove MSI2 gene

variants/filter_cnvkit.pl

@@ -54,7 +54,7 @@ while (my $line = <CNR>) {
     } else {
 	my @ids = split(/,/,$geneids);
 	foreach my $gid (@ids) {
-	    next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI/);
+	    next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI:/);
 	    my ($gene,@other) = split(/:/,$gid);
 	    my ($gname,@loc) = split(/_/,$gene);
 	    $genes{$gname} = 1;
@@ -93,7 +93,7 @@ while (my $line = <IN>) {
     } else {
 	my @ids = split(/,/,$geneids);
 	foreach my $gid (@ids) {
-	    next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI/);
+	    next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI:/);
 	    my ($gene,@other) = split(/:/,$gid);
 	    my ($gname,@loc) = split(/_/,$gene);
 	    $genes{$gname} = 1;

variants/somatic_vc.sh

@@ -90,6 +90,7 @@ baseDir="`dirname \"$0\"`"
 
 source /etc/profile.d/modules.sh
 module load htslib/gcc/1.8
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 
 if [ $algo == 'strelka2' ]
 then
@@ -140,7 +141,7 @@ then
   vcf-concat vscan*.vcf | vcf-sort | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter '((exists SOMATIC) & (GEN[*].DP >= 10))' | perl -pe "s/TUMOR/${tid}/" | perl -pe "s/NORMAL/${nid}/g" | bgzip >  ${pair_id}.varscan.vcf.gz
 elif [ $algo == 'shimmer' ]
 then
-    module load shimmer/0.1.1 samtools/gcc/1.8  vcftools/0.1.14
+    module load samtools/gcc/1.8  R/3.6.1-gccmkl vcftools/0.1.14
     shimmer.pl --minqual 25 --ref ${reffa} ${normal} ${tumor} --outdir shimmer 2> shimmer.err
     perl $baseDir/add_readct_shimmer.pl
     module rm java/oracle/jdk1.7.0_51