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# Cancer tumor/normal calling evaluation using synthetic dataset 3
# from the ICGC-TCGA DREAM challenge:
# https://www.synapse.org/#!Synapse:syn312572/wiki/62018
---
details:
- algorithm:
aligner: bwa
mark_duplicates: true
remove_lcr: true
variantcaller: [mutect2, freebayes, vardict, varscan]
ensemble:
numpass: 2
variant_regions: ../input/NGv3.bed
# svcaller: [cnvkit, lumpy, delly]
# coverage_interval: amplicon
analysis: variant2
description: syn3-normal
#files: ../input/synthetic.challenge.set3.normal.bam
files:
- ../input/synthetic_challenge_set3_normal_NGv3_1.fq.gz
- ../input/synthetic_challenge_set3_normal_NGv3_2.fq.gz
genome_build: GRCh37
metadata:
batch: syn3
phenotype: normal
- algorithm:
aligner: bwa
mark_duplicates: true
remove_lcr: true
variantcaller: [mutect2, freebayes, vardict, varscan]
ensemble:
numpass: 2
variant_regions: ../input/NGv3.bed
validate: ../input/synthetic_challenge_set3_tumor_20pctmasked_truth.vcf.gz
validate_regions: ../input/synthetic_challenge_set3_tumor_20pctmasked_truth_regions.bed
# svcaller: [cnvkit, lumpy, delly]
# coverage_interval: amplicon
# svvalidate:
# DEL: ../input/synthetic_challenge_set3_tumor_20pctmasked_truth_sv_DEL.bed
# DUP: ../input/synthetic_challenge_set3_tumor_20pctmasked_truth_sv_DUP.bed
# INS: ../input/synthetic_challenge_set3_tumor_20pctmasked_truth_sv_INS.bed
# INV: ../input/synthetic_challenge_set3_tumor_20pctmasked_truth_sv_INV.bed
analysis: variant2
description: syn3-tumor
#files: ../input/synthetic.challenge.set3.tumor.bam
files:
- ../input/synthetic_challenge_set3_tumor_NGv3_1.fq.gz
- ../input/synthetic_challenge_set3_tumor_NGv3_2.fq.gz
genome_build: GRCh37
metadata:
batch: syn3
phenotype: tumor
fc_date: '2014-08-13'
fc_name: dream-syn3
upload:
dir: ../final