Transform VCF file for Rqtl input for genetic mapping

[raj2010]

Hi everyone,

I am trying to find out if there is any tools out there to transform a VCF file to make input file for Rqtl or similar tool.
Basically, I have WGS for RIL population (180 lines) for which I did variant calling using samtools and have a VCF file that i need to parse it to get an input file for linkage/QTL mapping tools such as Rqtl or QTL cartographer. Please suggest if there are any tools. Any help is appreciated.

Thank you.

-Raj

[SNPsaurus]

Here's a python script that may be what you want:

https://github.com/brantp/rtd/blob/master/vcf_to_rqtl.py

[lindenb]

cross posted https://www.biostars.org/p/150009/