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How to get SNPs genotype matrix from vcf file for JoinMap analysis?

Hi, I need to use JoinMap for linkage map construction from GBS SNPs data. I need to get genotype matrix prior loading into the JoinMap. Is there any way to get genotype matrix from vcf file? Thanks in advance.

snp next-gen r
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updated by samadirn • samadirn • written by gaurab.bhattarai46 • gaurab.bhattarai46

Hi Gaurab,

I know it has been 5 years, but did you figure out how to do the conversion? I am having the same problem; I was wondering if you can help me with that.

Thank you.

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written by samadirn • samadirn

3 answers

you can use bcftools --view options to convert vcf file format to genotype file format

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written by binodregmi30 • binodregmi30

bcftools query was precisely designed to generate this kind of genotype tables.

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written by Jorge Amigo Jorge Amigo

Please try this script.

https://github.com/johnomics/scripts/blob/master/convert_vcf_to_joinmap.pl

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written by Jack • Jack

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