update strelka file

variants/germline_vc.sh

@@ -100,7 +100,7 @@ then
     for i in *.bam; do
     bamlist="$bamlist --bam ${PWD}/${i}"
     done
-    cut -f 1 $fbsplit | parallel --delay 1 --jobs 0 "freebayes -f ${index_path}/genome.fa  --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
+    cut -f 1 $fbsplit | parallel --memfree 2G --delay 1 --jobs 0 "freebayes -f ${index_path}/genome.fa  --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
     vcf-concat fb.*.vcf | vcf-sort | vcf-annotate -n --fill-type | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.fb.vcf.gz -
 elif [[ $algo == 'platypus' ]]
 then
@@ -143,7 +143,15 @@ then
     opt=''
     if [[ -n $tbed ]]
     then
-	opt="--callRegions ${tbed}.gz"
+	if [[ -f "${tbed}.gz" ]]
+	then
+	    opt="--callRegions ${tbed}.gz"
+	else
+	    cp $tbed panel.bed
+	    bgzip panel.bed
+	    tabix panel.bed.gz
+	    opt="--callRegions panel.bed.gz"
+	fi
     fi
     if [[ $rna == 1 ]]
     then

variants/somatic_vc.sh

@@ -103,14 +103,14 @@ then
     opt=''
     if [[ -n $tbed ]]
     then
-	if [[ -f $tbed ]]
+	if [[ -f "${tbed}.gz" ]]
 	then
 	    opt="--callRegions ${tbed}.gz"
 	else
-	    cp $tbed targetpanel.bed
-	    bgzip targetpanel.bed
-	    tabix targetpanel.bed.gz
-	    opt="--callRegions targetpanel.bed.gz"
+	    cp $tbed panel.bed
+	    bgzip panel.bed
+	    tabix panel.bed.gz
+	    opt="--callRegions panel.bed.gz"
 	fi
     fi
     mkdir manta