Description

Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

query_vcf (file)

VCF/GVCF file to query

*.{gvcf,vcf}.gz

truth_vcf (file)

gold standard VCF file

*.{gvcf,vcf}.gz

regions_bed (file)

Sparse regions to restrict the analysis to

*.bed

targets_bed (file)

Dense regions to restrict the analysis to

*.bed

fasta (file)

FASTA file of the reference genome

*.{fa,fasta}

fasta_fai (file)

The index of the reference FASTA

*.fai

false_positives_bed (file)

False positive / confident call regions. Calls outside these regions will be labelled as UNK.

*.{bed,bed.gz}

stratification_tsv (file)

Ambiguous region bed file(s)

*.bed

bams (file)

one or more BAM files for feature table extraction

*.bam

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

features (file)

One or more than one (if AF count is on ) CSV file containing feature information

*.features.csv

metrics (file)

One or more than one (if AF count is on ) JSON file with metrics

*.metrics.json

stats (file)

One or more than one (if AF count is on ) CSV file with benchmark stats

*.stats.csv

versions (file)

File containing software versions

versions.yml
included in
variantbenchmarking
maintainer
Github user kubranarci
get in touch
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Tools