1 changed files with 7 additions and 1 deletions
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tasks/VEP.wdl
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| String fasta | String fasta | ||||
| String vep_path | String vep_path | ||||
| File cache | File cache | ||||
| String ncbi_build | |||||
| String hg | |||||
| String species | String species | ||||
| String vcf2maf_path | String vcf2maf_path | ||||
| String docker | String docker | ||||
| 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 | |||||
| if [ hg == "hg19" ]; then | |||||
| ncbi_build="GRCh37" | |||||
| elif [ hg == "hg38" ]; then | |||||
| 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` | ||||
| if [ $ncol -lt 11 ]; then | if [ $ncol -lt 11 ]; then | ||||
| vcf2maf_ID="--tumor-id ${tumor_id} --normal-id ${normal_id}" | vcf2maf_ID="--tumor-id ${tumor_id} --normal-id ${normal_id}" |
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