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tasks/VEP.wdl
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| awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf | awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf | ||||
| # Define ncbi_build | # Define ncbi_build | ||||
| if [ hg == "hg19" ]; then | |||||
| if [ ${hg} == "hg19" ]; then | |||||
| ncbi_build="GRCh37" | ncbi_build="GRCh37" | ||||
| elif [ hg == "hg38" ]; then | |||||
| elif [ ${hg} == "hg38" ]; then | |||||
| ncbi_build="GRCh38" | ncbi_build="GRCh38" | ||||
| ncol=`awk -F'\t' '{if($1!~"^#"){print NF}}' ${basename}.PASS.vcf | uniq` | ncol=`awk -F'\t' '{if($1!~"^#"){print NF}}' ${basename}.PASS.vcf | uniq` |
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