Question

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

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6.6 years ago

gaurab.bhattarai46 ▴ 10

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 • 3.5k views

ADD COMMENT • link updated 13 months ago by samadirn • 0 • written 6.6 years ago by gaurab.bhattarai46 ▴ 10

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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.

ADD REPLY • link 13 months ago by samadirn • 0

score 0 · Answer 1 · 2021-04-24

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3.7 years ago

binodregmi30 ▴ 10

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

ADD COMMENT • link 3.7 years ago by binodregmi30 ▴ 10

score 0 · Answer 2 · 2021-04-25

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3.7 years ago

Jorge Amigo 14k

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

ADD COMMENT • link 3.7 years ago by Jorge Amigo 14k

score 0 · Answer 3 · 2022-09-14

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2.3 years ago

Jack ▴ 10

Please try this script.

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

ADD COMMENT • link 2.3 years ago by Jack ▴ 10