Description

A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

VCF file

*.{vcf,.vcf.gz}

tbi{:bash}

:file

TBI file

af_file{:bash}

:file

Read allele frequencies from a tab-delimited file containing the columns: CHROM POS REF,ALT AF.

af_file_tbi{:bash}

:file

tbi index of af_file.

genetic_map{:bash}

:file

Genetic map in the format required also by IMPUTE2.

regions_file{:bash}

:file

Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default).

samples_file{:bash}

:file

File of sample names to include or exclude if prefixed with ’^’.

targets_file{:bash}

:file

Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default).

Output

name:type
description
pattern

roh{:bash}

meta{:bash}

:map

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

*.roh{:bash}

:file

Contains site-specific and/or per-region runs of homo/autozygosity calls.

*.{roh}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

roh
MIT

A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.

htslib.org http://www.htslib.org/doc/bcftools 10.1093/bioinformatics/btp352
included in
raredisease
maintainer
Github user ramprasadn
get in touch
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