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---
dir:
out: test/data/method
prep: test/data/method/prep
experiments:
- sample: Test1
ref: test/data/GRCh37.fa
#intervals: test/data/target-regions.bed
calls:
- name: gatk
metadata:
aligner: novoalign
caller: gatk
technology: illumina
file: test/data/gatk-calls.vcf
align: test/data/aligned-reads.bam
remove-refcalls: true
normalize: false
annotate: true
- name: freebayes
metadata:
aligner: novoalign
caller: freebayes
technology: illumina
file: test/data/freebayes-calls.vcf
align: test/data/aligned-reads.bam
annotate: true
filters:
- HRun > 5.0
- QD < 2.0
- FS > 60.0
- MQRankSum < -12.5
- name: cg
metadata:
aligner: cg
caller: cg
technology: cg
prep: true
fix-sample-header: true
file: test/data/cg-calls.vcf
finalize:
- method: multiple
target: gatk
- method: recal-filter
target: [gatk, freebayes]
params:
filters: [HRun > 5.0]
classifiers: [AD, DP, QUAL, PL, gms_illumina]
xspecific: true
trusted:
total: 0.75
technology: 0.65
- method: validate
target: gatk
params:
filters:
keep: [QD < 10.0]
validate: [QD > 10.0]
validate:
approach: random
count: 1
top-metric:
- name: "QD"
mod: -1
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