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

meta (map)

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

versions (file)

File containing software versions

versions.yml

hbd (file)

contains HBD segments within individuals

*.hbd.gz

ibd (file)

contains IBD segments shared between individuals

*.ibd.gz

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
maintainer
Github user ashotmarg
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

hapibd
Apache-2.0

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

github.com/browning-lab/hap-ibd/blob/master/README.md 10.1016/j.ajhg.2020.02.010