phase_common

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Description

Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.

Usage

Simple run

SHAPEIT5_phase_common --input 10k/msprime.nodup.bcf --filter-maf 0.001  --output 10k/msprime.common.phased.bcf --region 1 --thread 8

The program phases common variants (--filter-maf 0.001) from the input file (--input 10k/msprime.nodup.bcf) using 8 threads (--thread 8) on the full chromosome 1 (--region 1) and saves the results in the output file (--output 10k/msprime.common.phased.bcf).

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
-I [--input ] STRING NA Genotypes to be phased in VCF/BCF format
-H [--reference ] STRING NA Reference panel of haplotypes in VCF/BCF format
-S [--scaffold ] STRING NA Scaffold of haplotypes in VCF/BCF format
-M [--map ] STRING NA Genetic map
--pedigree STRING NA Pedigree information (chile father mother)
-R [--region ] STRING NA Target region

Filter parameters

Option name Argument Default Description
--filter-snp NA NA If specified, the program only consider SNPs
--filter-maf FLOAT 0 [Expert option] Only consider variants with MAF above the specifeed value. It requires AC/AN tags in VCF/BCF file.

MCMC parameters

Option name Argument Default Description
--mcmc-iterations STRING 5b,1p,1b,1p,1b,1p,5m Iteration scheme of the MCMC (burnin=b, pruning=p, main=m)
--mcmc-prune FLOAT 0.999 Pruning threshold for genotype graphs
--mcmc-noinit NA NA If specified, phasing initialization by PBWT sweep is disabled

PBWT parameters

Option name Argument Default Description
--pbwt-modulo FLOAT 0.1 Storage frequency of PBWT indexes in cM
--pbwt-depth INT 4 Depth of PBWT indexes to condition on
--pbwt-mac INT 5 Minimal Minor Allele Count at which PBWT is evaluated
--pbwt-mdr FLOAT 0.1 Maximal Missing Data Rate at which PBWT is evaluated
--pbwt-window INT 4 Run PBWT selection in windows of this size

HMM parameters

Option name Argument Default Description
--hmm-window INT 4 Minimal size of the phasing window in cM
--hmm-ne 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-graph STRING NA Phased haplotypes in BIN format (Useful to sample multiple likely haplotype configurations per sample)
--log STRING NA Log file