update determine tid

variants/svcalling.sh

@@ -66,14 +66,19 @@ then
 fi
 mkdir -p temp
 
-if [[ -z $tid ]]
+if [[ -z $tid ]] && [[ -f ${sbam} ]]
 then
     tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
 fi
 
 bams=''
 for i in *.bam; do
-    bams="$bams $i" 
+    bams="$bams $i"
+    sid=`samtools view -H ${i} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+    if [[ $sid =~ "_T_" ]]
+    then
+	tid=$sid
+    fi
 done
 
 #RUN DELLY
@@ -92,6 +97,7 @@ then
     then
 	zcat ${pair_id}.delly.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHR2 END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u > ${pair_id}.dgf.txt
 	mv ${pair_id}.delly.vcf.gz ${pair_id}.delly.ori.vcf.gz
+	echo "perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz"
 	perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz
 	bgzip -f ${pair_id}.delly.vcf
 	zgrep '#CHROM' ${pair_id}.delly.vcf.gz > ${pair_id}.delly.genefusion.txt