Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts

variants/norm_annot.sh

@@ -15,6 +15,7 @@ do
     case $opt in
         p) pair_id=$OPTARG;;
 	v) vcf=$OPTARG;;
+	r) index_path=$OPTARG;;
         h) usage;;
     esac
 done
@@ -25,6 +26,15 @@ baseDir="`dirname \"$0\"`"
 source /etc/profile.d/modules.sh
 module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q 
 
+if [[ -a "${index_path}/genome.fa" ]]
+then
+    reffa="${index_path}/genome.fa"
+    dict="${index_path}/genome.dict"
+else 
+    echo "Missing Fasta File: ${index_path}/genome.fa"
+    usage
+
+fi
 
 perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf
 bgzip -f ${pair_id}.uniform.vcf

variants/pindel.sh

@@ -61,5 +61,12 @@ tabix pindel.vcf.gz
 bash $baseDir/norm_annot.sh -r ${index_path} -p pindel -v pindel.vcf.gz
 perl $baseDir/parse_pindel.pl ${pair_id} pindel.norm.vcf.gz
 java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.indel.vcf |bgzip > ${pair_id}.pindel_indel.vcf.gz
-java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.dup.vcf | bedtools intersect -header -b ${idtbed} -a stdin | bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
+
+if [[ -a $idtbed ]]
+then
+    java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.dup.vcf | bedtools intersect -header -b ${idtbed} -a stdin | bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
+else
+    java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.dup.vcf | bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
+fi
+
 java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.sv.vcf | bgzip > ${pair_id}.pindel_sv.vcf.gz