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pbwtutil

Utilities for working with the PBWT format

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The pbwtutil software leverages the libpbwt library to perfrom five main functions:

  1. coancestry: produce a pairwise match sharing similarity matrix between all diploid individuals in the PBWT
  2. convert: convert a data set from either PLINK or VCF to the PBWT format
  3. match: run matching on a PBWT data set by marking a haplotype as the query
  4. pileup: calculate match pileup depth across chromosomes
  5. summary: report on basic statistics of a PBWT file
  6. view: view the contents of a PBWT file

coancestry function

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

convert function

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

match function

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

pileup function

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

summary function

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

view function

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

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Utilities for working with the PBWT format

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