phase_rare

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Table of contents

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Description

Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate).

Usage

Simple run

#chunk1
SHAPEIT5_phase_rare --input-plain 10k/msprime.nodup.bcf --scaffold 10k/msprime.common.truth.bcf --output 10k/msprime.rare.chunk1.bcf --scaffold-region 1:1000000-3000000 --input-region 1:1500000-2500000 --thread 8

#chunk2
SHAPEIT5_phase_rare --input-plain 10k/msprime.nodup.bcf --scaffold 10k/msprime.common.truth.bcf --output 10k/msprime.rare.chunk2.bcf --scaffold-region 1:2000000-4000000 --input-region 1:2500001-3500000 --thread 8

The first command phases rare variants from the input file (--input-plain 10k/msprime.nodup.bcf) using 8 threads (--thread 8) on the region 1500000-2500000 of chromosome 1 (--input-region 1:1500000-2500000) using a haplotype scaffold phased for the full chromosome 1 obtained from the phase_common program in the region 1000000-3000000 of chromosome 1 (--scaffold-region 1:1000000-3000000) and saves the results in the output file (--output 10k/msprime.rare.chunk1.bcf).

The obtained files can be quickly concatenated to generate chromosome-wide files using bcftools concat –naive.

Command line options

Basic options

Option name Argument Default Description
--help NA NA Produces help message
--seed INT 15052011 Seed of the random number generator
-T [ --thread ] INT 1 Number of thread used

Input files

Option name Argument Default Description
--input-plain STRING NA Genotypes to be phased in plain VCF/BCF format
--input-region STRING NA Region to be considered in --input-plain
--input-maf FLOAT 0.001 Threshold for sparse genotype representation in –input-plain
--scaffold STRING NA Scaffold of haplotypes in VCF/BCF format
--scaffold-region STRING NA Region to be considered in --scaffold
--map STRING NA Genetic map
--pedigree STRING NA Pedigree information (chile father mother)

PBWT parameters

Option name Argument Default Description
--pbwt-modulo FLOAT 0.1 Storage frequency of PBWT indexes in cM
--pbwt-depth-common INT 2 Depth of PBWT indexes at common sites to condition on
--pbwt-depth-rare INT 2 Depth of PBWT indexes at rare sites to condition on
--pbwt-mac INT 2 Minimal Minor Allele Count at which PBWT is evaluated
--pbwt-mdr FLOAT 0.1 Maximal Missing Data Rate at which PBWT is evaluated

HMM parameters

Option name Argument Default Description
--effective-size INT 15000 Effective size of the population

Output files

Option name Argument Default Description
-O [--output ] STRING NA Phased haplotypes in VCF/BCF format
--output-buffer STRING NA If specified, right and left buffers are printed in output
--log STRING NA Log file