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tasks/Haplotyper.wdl
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| @@ -30,13 +30,6 @@ task Haplotyper { | |||
| INTERVAL="" | |||
| fi | |||
| if [ ${pon_vcf} ]; then | |||
| PON="--pon ${pon_vcf}" | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${pon_vcf} | |||
| else | |||
| PON="" | |||
| fi | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \ | |||
| --interval ${regions} -r ${ref_dir}/${fasta} \ | |||
| -i ${recaled_bam} -q ${recal_table}\ | |||
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