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{:bash}

:map

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

query_vcf{:bash}

:file

VCF/GVCF file to query

*.{gvcf,vcf}.gz

truth_vcf{:bash}

:file

gold standard VCF file

*.{gvcf,vcf}.gz

regions_bed{:bash}

:file

Sparse regions to restrict the analysis to

*.bed

targets_bed{:bash}

:file

Dense regions to restrict the analysis to

*.bed

meta2{:bash}

:map

Groovy Map containing fasta file information e.g. [ id:‘test2’]

fasta{:bash}

:file

FASTA file of the reference genome

*.{fa,fasta}

meta3{:bash}

:map

Groovy Map containing fai file information e.g. [ id:‘test3’]

fasta_fai{:bash}

:file

The index of the reference FASTA

*.fai

meta4{:bash}

:map

Groovy Map containing false_positives_bed file information e.g. [ id:‘test4’]

false_positives_bed{:bash}

:file

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

*.{bed,bed.gz}

meta5{:bash}

:map

Groovy Map containing ambiguous_beds file information e.g. [ id:‘test5’]

ambiguous_beds{:bash}

:file

Ambiguous regions

*.{bed,bed.gz}

meta6{:bash}

:map

Groovy Map containing bam file information e.g. [ id:‘test6’]

bams{:bash}

:file

one or more BAM files for feature table extraction

*.bam

Output

name:type
description
pattern

features{:bash}

meta{:bash}

:map

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

*.features.csv{:bash}

:file

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

*.features.csv

metrics{:bash}

meta{:bash}

:map

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

*.metrics.json{:bash}

:file

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

*.metrics.json

stats{:bash}

meta{:bash}

:map

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

*.stats.csv{:bash}

:file

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

*.stats.csv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
variantbenchmarking
maintainer
Github user kubranarci
get in touch
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