Description

The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples.

Input

name:type
description
pattern

meta:map

Groovy Map containing cohort information e.g. [ id:‘test’ ]

vcf:file

phased VCF file with a GT FORMAT subfield with no missing alleles

*.{vcf,vcf.gz}

map:file

genetic map with cM units in PLINK format

*.{map,map.gz,map.zip}

exclude:file

text file containing samples one sample per line to be excluded from the analysis

*.*

Output

name:type
description
pattern

hbd

meta:map

Groovy Map containing cohort information e.g. [ id:‘test’ ]

*.hbd.gz:file

contains HBD segments within individuals

*.hbd.gz

ibd

meta:map

Groovy Map containing cohort information e.g. [ id:‘test’ ]

*.ibd.gz:file

contains IBD segments shared between individuals

*.ibd.gz

log

meta:map

Groovy Map containing cohort information e.g. [ id:‘test’ ]

*.log:file

contains a summary of the analysis which includes the analysis parameters the number of markers the number of samples the number of output HBD and IBD segments and the mean number of HBD and IBD segments per sample

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

hapibd
Apache-2.0

Hap-ibd Detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data.