2 changed files with 3 additions and 3 deletions
BIN
.DS_Store
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+ 3
- 3
tasks/PON.wdl
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| @@ -26,13 +26,13 @@ task PoN { | |||
| cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/ | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf} | |||
| # Generating TNhaplotyper PON | |||
| # Generating TNhaplotyper PoN | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_TNhaplotyper_pon.vcf | |||
| # Generating TNhaplotyper2 PON | |||
| # Generating TNhaplotyper2 PoN | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper2 --normal_sample ${sample} ${sample}_TNhaplotyper2_pon.vcf | |||
| # Generating TNscope PON | |||
| # Generating TNscope PoN | |||
| ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNscope --normal_sample ${sample} ${sample}_TNscope_pon.vcf | |||
| >>> | |||
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