Transform VCF file for Rqtl input for genetic mapping

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8.8 years ago

rajini28m ▴ 10

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

SNP • 5.2k views

ADD COMMENT • link updated 16 months ago by Ram 43k • written 8.8 years ago by rajini28m ▴ 10

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Hello rajini28m!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=61076

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLY • link updated 16 months ago by Ram 43k • written 8.8 years ago by Pierre Lindenbaum 161k

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Hi Pierre,

Oops I did not realize that. Sorry. Thanks for the reply though.

It will not happen again.

Raj

ADD REPLY • link updated 16 months ago by Ram 43k • written 8.8 years ago by rajini28m ▴ 10

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