Utilities for working with the PBWT format
The pbwtutil
software leverages the libpbwt
library to perfrom five main functions:
coancestry
: produce a pairwise match sharing similarity matrix between all diploid individuals in the PBWTconvert
: convert a data set from either PLINK or VCF to the PBWT formatmatch
: run matching on a PBWT data set by marking a haplotype as the querypileup
: calculate match pileup depth across chromosomessummary
: report on basic statistics of a PBWT fileview
: view the contents of a PBWT file
Usage: pbwtutil coancestry [OPTION]... [PBWT FILE]
Produce coancestry matrix for all samples in PBWT
Options:
--adjlist Output graph-based adjacency list [ Default: False ]
--diploid Output diploid rather than haploid-based measures
--set Find only set-maximal matches [ Default: all matches ]
--sites Print site indices [ Default: false ]
--count Coancestry matrix will have match count [ Default: total length ]
--minlen FLOAT Minimum match size (cM) [ Default: 0.5 cM ]
--version Print version number and exit
--help Display this help message and exit
Usage: pbwtutil convert [OPTION]... [INPUT STUB]
Convert PLINK or VCF to PBWT or vice versa
Options:
--phased Input data are phased
--vcf Input file is VCF format
--map <FILE> Popmap file (for VCF input)
--reg Input PLINK stub includes a REG file
--out <STR> Output stub (.pbwt extension will be added)
--query <STR> Use only this region/population (requires -r switch)
--version Print version number and exit
--help Display this help message and exit
Usage: pbwtutil match [OPTION]... [PBWT FILE]
Retrieve match sets in PBWT using query
Options:
--minlen FLOAT Minimum match size (cM) [ Default: 0.5 cM ]
--query STR String identifier of haplotypes to mark as query
--all Print a list of all individual matches with query
--set Find only set-maximal matches [ Default: all matches ]
--sites Print site indices [ Default: false ]
--version Print version number and exit
--help Display this help message and exit
Usage: pbwtutil pileup [OPTION]... [PBWT FILE]
Calculate match pileup depth across chromosomes
Options:
--minlen FLOAT Minimum match size (cM) [ Default: 0.5 cM ]
--query STR String identifier of haplotypes to mark as query
--set Find only set-maximal matches [ Default: all matches ]
--version Print version number and exit
--help Display this help message and exit
Usage: pbwtutil summary [OPTION]... [PBWT FILE]
Print report describing pbwt file
Options:
--regcount Print region sizes
--version Print version number and exit
--help Display this help message and exit
Usage: pbwtutil view [OPTION]... [PBWT FILE]
Print contents of .pbwt file to stdout
Options:
--nohaps Omit haplotype states-- only print sample metadata
--sites Print only site information
--version Print version number and exit
--help Display this help message and exit