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# Example configuration to perform variant calling with multiple methods on a set of
# NA12878 replicates. The final calls are merged into a finalized ensemble callset
# using a support vector machine based on several classifier metrics.
---
fc_date: '121119'
fc_name: cliacmp
details:
- files: [/usr/local/projects/CLIA-Validation/secondary/NA12878-NGv3-LAB1360-A/alignment/NA12878-NGv3-LAB1360-A.bam]
lane: NA12878-NGv3-LAB1360-A
description: NA12878-NGv3-LAB1360-A
analysis: variant
genome_build: GRCh37
algorithm:
aligner: false
recalibrate: false
realign: false
variantcaller: [gatk, freebayes, samtools, gatk-haplotype, varscan]
ensemble:
format-filters: [DP < 4]
classifiers:
balance: [AD, FS, Entropy]
calling: [ReadPosEndDist, PL, PLratio, Entropy, NBQ]
classifier-params:
type: svm
trusted-pct: 0.65
quality_format: Standard
coverage_interval: regional
variant_regions: /usr/local/projects/CLIA-Validation/secondary/NA12878-NGv3-LAB1360-A/enrichment/padded_targets_200.bed
- files: [/usr/local/projects/CLIA-Validation/secondary/NA12878-NGv3-LAB1363-A/alignment/NA12878-NGv3-LAB1363-A.bam]
lane: NA12878-NGv3-LAB1363-A
description: NA12878-NGv3-LAB1363-A
analysis: variant
genome_build: GRCh37
algorithm:
aligner: false
recalibrate: false
realign: false
variantcaller: [gatk, freebayes, samtools, gatk-haplotype, varscan]
ensemble:
format-filters: [DP < 4]
classifiers:
balance: [AD, FS, Entropy]
calling: [ReadPosEndDist, PL, PLratio, Entropy, NBQ]
classifier-params:
type: svm
trusted-pct: 0.65
quality_format: Standard
coverage_interval: regional
variant_regions: /usr/local/projects/CLIA-Validation/secondary/NA12878-NGv3-LAB1363-A/enrichment/padded_targets_200.bed
- files: [/usr/local/projects/CLIA-Validation/secondary/NA12878-AGXT2-LAB1368-A/alignment/NA12878-AGXT2-LAB1368-A.bam]
lane: NA12878-AGXT2-LAB1368-A
description: NA12878-AGXT2-LAB1368-A
analysis: variant
genome_build: GRCh37
algorithm:
aligner: false
recalibrate: false
realign: false
variantcaller: [gatk, freebayes, samtools, gatk-haplotype, varscan]
ensemble:
format-filters: [DP < 4]
classifiers:
balance: [AD, FS, Entropy]
calling: [ReadPosEndDist, PL, PLratio, Entropy, NBQ]
classifier-params:
type: svm
trusted-pct: 0.65
quality_format: Standard
coverage_interval: regional
variant_regions: /usr/local/projects/CLIA-Validation/secondary/NA12878-AGXT2-LAB1368-A/enrichment/padded_targets_200.bed
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