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tasks/VEP.wdl
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| @@ -42,7 +42,7 @@ task VEP { | |||
| if [ $normal_id ]; then | |||
| SAMPLE_vcf2maf="--tumor-id $tumor_id --normal-id $normal_id" | |||
| SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id --vcf-normal-id $normal_id" | |||
| cp ${vcf} ${sample_id}.tmp.vcf | |||
| cp ${vcf} ${sample_id}.tmp1.vcf | |||
| else | |||
| SAMPLE_vcf2maf="--tumor-id $tumor_id" | |||
| # Add a column and remove it after vcf2vcf | |||
| @@ -62,7 +62,7 @@ task VEP { | |||
| cp ${sample_id}.tmp2.vcf ${basename}.norm.vcf | |||
| else | |||
| cut -f 1,2,3,4,5,6,7,8,9,10 ${sample_id}.tmp2.vcf > ${basename}.norm.vcf | |||
| fi | |||
| # VEP annotation | |||
| echo "VEP annotation..." | |||
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