Description

Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.

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 stratification_tsv file information e.g. [ id:‘test5’]

stratification_tsv{:bash}

:file

Stratification file list in TSV format

*.tsv

meta6{:bash}

:map

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

stratification_beds{:bash}

:file

One or more BED files used for stratification (these should be referenced in the stratification TSV)

*.bed

Output

name:type
description
pattern

summary_csv{:bash}

meta{:bash}

:map

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

*.summary.csv{:bash}

:file

A CSV file containing the summary of the benchmarking

*.summary.csv

roc_all_csv{:bash}

meta{:bash}

:map

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

*.roc.all.csv.gz{:bash}

:file

A CSV file containing ROC values for all variants

*.roc.all.csv.gz

roc_indel_locations_csv{:bash}

meta{:bash}

:map

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

*.roc.Locations.INDEL.csv.gz{:bash}

:file

A CSV file containing ROC values for all indels

*.roc.Locations.INDEL.csv.gz

roc_indel_locations_pass_csv{:bash}

meta{:bash}

:map

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

*.roc.Locations.INDEL.PASS.csv.gz{:bash}

:file

A CSV file containing ROC values for all indels that passed all filters

*.roc.Locations.INDEL.PASS.csv.gz

roc_snp_locations_csv{:bash}

meta{:bash}

:map

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

*.roc.Locations.SNP.csv.gz{:bash}

:file

A CSV file containing ROC values for all SNPs

*.roc.Locations.SNP.csv.gz

roc_snp_locations_pass_csv{:bash}

meta{:bash}

:map

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

*.roc.Locations.SNP.PASS.csv.gz{:bash}

:file

A CSV file containing ROC values for all SNPs that passed all filters

*.roc.Locations.SNP.PASS.csv.gz

extended_csv{:bash}

meta{:bash}

:map

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

*.extended.csv{:bash}

:file

A CSV file containing extended info of the benchmarking

*.extended.csv

runinfo{:bash}

meta{:bash}

:map

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

*.runinfo.json{:bash}

:file

A JSON file containing the benchmarking metrics

*.metrics.json.gz

metrics_json{:bash}

meta{:bash}

:map

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

*.metrics.json.gz{:bash}

:file

A JSON file containing the run info

*.runinfo.json

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

An annotated VCF

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.tbi{:bash}

:file

The index of the annotated VCF

*.tbi

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
variantbenchmarking
maintainer
Github user nvnieuwk
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