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tasks/picard.wdl
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| @@ -14,7 +14,7 @@ task picard { | |||
| set -o pipefail | |||
| set -e | |||
| nt=$(nproc) | |||
| java -jar /usr/bin/picard/picard.jar LiftoverVcf INPUT=${vcf} OUTPUT=${sample}_picard.vcf REJECT=rejected_variants.vcf CHAIN=${chain_dir}/${chain} R=${ref_dir}/${fasta} | |||
| java -jar /usr/bin/picard/picard.jar LiftoverVcf -INPUT ${vcf} -OUTPUT ${sample}_picard.vcf -REJECT rejected_variants.vcf -CHAIN ${chain_dir}/${chain} -R ${ref_dir}/${fasta} | |||
| #java -jar /usr/bin/picard/picard.jar LiftoverVcf -I ${vcf} -O ${sample}_picard.vcf -REJECT rejected_variants.vcf -CHAIN ${chain_dir}/${chain} -R ${ref_dir}/${fasta} | |||
| >>> | |||
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