Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

VCF file

*.{vcf,.vcf.gz}

af_file (file)

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

af_file_tbi (file)

tbi index of af_file.

genetic_map (file)

Genetic map in the format required also by IMPUTE2.

regions_file (file)

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

samples_file (file)

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

targets_file (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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

roh (file)

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

*.{roh}
included in
raredisease
maintainer
Github user ramprasadn
get in touch
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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