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tasks/picard.wdl
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| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| 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} | |||||
| #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} | |||||
| LiftoverVcf -I ${vcf} -O ${sample}_picard.vcf -REJECT rejected_variants.vcf -CHAIN ${chain_dir}/${chain} -R ${ref_dir}/${fasta} | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
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