modules/happy_sompy

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

happysompybenchmarkhaplotypevalidationsomatic variants

https://github.com/nf-core/modules/[...]/modules/nf-core/happy/sompy

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

Tools

sompy
BSD-2-clause

Haplotype VCF comparison tools somatic variant comparison

illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking github.com/Illumina/hap.py/blob/master/doc/sompy.md https://github.com/Illumina/hap.py

modules/happy_sompy

Description

Input

`meta:map`

`query_vcf:file`

`truth_vcf:file`

`regions_bed:file`

`targets_bed:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fasta_fai:file`

`meta4:map`

`false_positives_bed:file`

`meta5:map`

`ambiguous_beds:file`

`meta6:map`

`bams:file`

Output

`features`

`meta:map`

`*.features.csv:file`

`metrics`

`meta:map`

`*.metrics.json:file`

`stats`

`meta:map`

`*.stats.csv:file`

`versions`

`versions.yml:file`

Tools

sompy
BSD-2-clause

included in

maintainer

get in touch

modules/happy_sompy

Description

Input

meta:map

query_vcf:file

truth_vcf:file

regions_bed:file

targets_bed:file

meta2:map

fasta:file

meta3:map

fasta_fai:file

meta4:map

false_positives_bed:file

meta5:map

ambiguous_beds:file

meta6:map

bams:file

Output

features

meta:map

*.features.csv:file

metrics

meta:map

*.metrics.json:file

stats

meta:map

*.stats.csv:file

versions

versions.yml:file

Tools

sompy BSD-2-clause

included in

maintainer

get in touch

`meta:map`

`query_vcf:file`

`truth_vcf:file`

`regions_bed:file`

`targets_bed:file`

`meta2:map`

`fasta:file`

`meta3:map`

`fasta_fai:file`

`meta4:map`

`false_positives_bed:file`

`meta5:map`

`ambiguous_beds:file`

`meta6:map`

`bams:file`

`features`

`meta:map`

`*.features.csv:file`

`metrics`

`meta:map`

`*.metrics.json:file`

`stats`

`meta:map`

`*.stats.csv:file`

`versions`

`versions.yml:file`

sompy
BSD-2-clause