updating git repo

alignment/bamqc.sh

@@ -8,7 +8,7 @@ usage() {
   echo "-n  --NucType"
   echo "-p  --Prefix for output file name"
   echo "-c  --Capture Bedfile"
-  echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -b SRR1551047.bam  -y dna -c target.bed"
+  echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -b SRR1551047.bam  -n dna -c target.bed"
   exit 1
 }
 OPTIND=1 # Reset OPTIND

variants/germline_vc.sh

@@ -106,7 +106,7 @@ then
     bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.platypus.vcf.gz platypus.vcf.gz
 elif [[ $algo == 'strelka2' ]]
 then
-    if [[ $rna==1 ]]
+    if [[ $rna == 1 ]]
     then
 	mode="--rna"
     else

variants/unionvcf.pl

@@ -38,9 +38,6 @@ foreach $vcf (@vcffiles) {
     }
     my ($chrom, $pos,$id,$ref,$alt,$score,
 	$filter,$annot,$format,@gts) = split(/\t/, $line);
-    if ($pos eq '90088702') {
-	warn "allele frequency\n";
-    }
     my %hash = ();
     foreach $a (split(/;/,$annot)) {
       my ($key,$val) = split(/=/,$a);
@@ -107,7 +104,7 @@ foreach $vcf (@vcffiles) {
   }
   close VCF;
 }
-my @callers = ('ssvar','platypus','sam','gatk','strelka2','hotspot');
+my @callers = ('ssvar','sam','gatk','strelka2','platypus','hotspot');
 if (grep(/mutect/,@vcffiles)) {
     @callers = ('sssom','pmutect','shimmer','strelka2','varscan','virmid');
 }