fitler virus, filter cna

alignment/virusalign.sh

@@ -49,5 +49,5 @@ samtools index ${pairid}.viral.bam
 samtools idxstats ${pairid}.viral.bam >${pairid}.viral.idxstats.txt
 if [[ $filter == 1 ]]
 then
-    perl $baseDir/filter_viral_idxstats.txt -p ${pairid} ${pairid}.viral.idxstats.txt
+    perl $baseDir/filter_viral_idxstats.pl -p ${pairid} ${pairid}.viral.idxstats.txt
 fi

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+$|^SNP:rs\d+$|^-$|Fusion/);
+	    next if ($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+$|^SNP:rs\d+$|^-$|Fusion/);
+	    next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI/);
 	    my ($gene,@other) = split(/:/,$gid);
 	    my ($gname,@loc) = split(/_/,$gene);
 	    $genes{$gname} = 1;