switchError

Compute switch error rates

This code was written by Olivier Delaneau with build environment and documentation contributions from Arjun Biddanda.

Building the executable

The environment to build the software can be conducted by conda env create -f env.yaml. You can then subsequently run conda activate switchError and make, which should build the executable for you in bin/switchError.

Input File Definitions

• "--gen": BCF formatted file of genotyped individuals [required]
• "--hap": BCF formatted file of individuals with estimated haplotypes [required]
• "--fam": PLINK formatted FAM file for evaluating IDs
• "--reg": BED-formatted region string for evaluating switch error rates [required]
• "--ps": Phase set information (more information here)
• "--out": output prefix, the outputfiles have extensions *.iser, *.vser,*.mser.gz [required]
• "--maf": minor allele frequency cutoff

Output File Definitions

1. *.iser

The columns in order are:

• individual index
• individual name
• number of mendel errors
• number of opportunities for mendel errors
• number of typing errors
• number of opportunities for typing errors
• number of switch errors
• number of opportunities for switch errors

2. *.vser

• variant-level index
• position of variant
• minor allele count
• minor allele frequency
• number of mendel errors
• number of opportunities for mendel errors
• number of typing errors
• number of opportunities for typing errors
• number of switch errors
• number of opportunities for switch errors

Across both settings, we largely want to look at how to use the last two columns and their distribution across individuals.