This is a basic tool written which can be used to convert phased genotypes in vcf format into the format used by chromopainter. It requires you to have R installed and Rscript in your path, as well a few libraries, which can be easily installed using install.packages(c("stringr", "data.table", "Rcpp", "optparse")).
The C++ code compiles on on macOS Catalina, Ubuntu 20+ and CentOS 7.9.2009 (Core).
This tool hasn't been tested thoroughly, so please email/message me if you use it and have any issues.
Usage: src/vcf_to_chromopainter_main.R [options]
Options:
-g CHARACTER, --genotypes=CHARACTER
genotype file name. no default - required
-l CHARACTER, --genotypelikelihoods=CHARACTER
genotype likelihoods file name
-u LOGICAL, --uncertaintyMode=LOGICAL
Run in uncertainty mode
-o CHARACTER, --output=CHARACTER
Output file stem. no default - required
-m CHARACTER, --genmap=CHARACTER
plink formatted genetic map
-h, --help
Show this help message and exit
If you want to make the input for ChromoPainter V2 (which is very likely), then run the above script like this:
Rscript vcf_to_chromopainter_main.R \
-g input.vcf \ ## this file should contain phased genotypes (e.g. '0|1')
-u FALSE \
-o output \
-m genetic_map.txt
You will need to download a genetic map for the relevant build and chromosome you are analysing. These can be downloaded from here https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/.