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

meta2:map

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

fasta:file

FASTA file of the reference genome

*.{fa,fasta}

meta3:map

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

fasta_fai:file

The index of the reference FASTA

*.fai

meta4:map

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

false_positives_bed:file

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

*.{bed,bed.gz}

meta5:map

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

ambiguous_beds:file

Ambiguous regions

*.{bed,bed.gz}

meta6:map

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

bams:file

one or more BAM files for feature table extraction

*.bam

Output

name:type
description
pattern

features

meta:map

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

]

*.features.csv:file

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

*.features.csv

metrics

meta:map

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

]

*.metrics.json:file

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

*.metrics.json

stats

meta:map

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

]

*.stats.csv:file

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

*.stats.csv

versions

versions.yml:file

File containing software versions

versions.yml