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Commit 0398b847 authored by Brandi Cantarel's avatar Brandi Cantarel
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make filtering pindel ITDs optional

parent 68aab844
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......@@ -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
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