switch

{: .no_toc .text-center }

Table of contents

{: .no_toc .text-delta }

  1. TOC {:toc}

Description

Program to compute switch error rate and genotyping error rate given simulated or trio data.

Usage

Simple run

SHAPEIT5_switch --validation 10k/msprime.nodup.bcf --estimation 10k/msprime.rare.chunk1.bcf --region 1 --output 10k/msprime.rare.chunk1

The program estimates errors from the phased file (--estimation 10k/msprime.rare.chunk1.bcf) on the full chromosome 1 (--region 1) using the a validation file --validation 10k/msprime.nodup.bcf) and saves the results in several output files with the specified prefix (--output 10k/msprime.rare.chunk1).

Command line options

Basic options

Option name Argument Default Description
--help NA NA Produces help message
-T [ --thread ] INT 1 Number of thread used

Input files

Option name Argument Default Description
-V [--validation ] STRING NA Validation dataset in VCF/BCF format
-E [--estimation ] STRING NA Phased dataset in VCF/BCF format
-F [--frequency ] STRING NA Variant frequency in VCF/BCF format
-P [--pedigree ] STRING NA Pedigree file in PED format
-R [--region ] STRING NA Target region
--nbins INT 20 Number of bins used for calibration
--min-pp FLOAT 0 Minimal PP value for entering computations
--singleton STRING NA Singleton phase
--dupid STRING NA Duplicate ID for UKB matching IDs

Output files

Option name Argument Default Description
-O [--output ] STRING NA Phased haplotypes in VCF/BCF format
--log STRING NA Log file