Question

Problem with vcf file columns

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2.5 years ago

Camila Martínez ▴ 40

Hello. I'm having troubles with a vcf file I just generated with Stacks. The thing is that the column of the first sample (the first individual in my vcf file) instead of having the information about the genotype, the depth and other things, it has the format in which the data is coded. The first sample is 070_sort, but the rest of the column has the format string instead of the actual information about the SNPs

The file hasn't been edited or filtered, Stacks outputted it just like this. I don't know how to fix this. I tried running a PCA on a vcf file derived from the one in the picture, and a lot of samples didn't behave as I expected. So I think it is because the markers aren't related with the correct sample.

I would appreciate any help. Thanks.

stacks vcf • 675 views

ADD COMMENT • link updated 2.5 years ago by Pierre Lindenbaum 161k • written 2.5 years ago by Camila Martínez ▴ 40

score 2 · Answer 1 · 2021-11-09

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2.5 years ago

Pierre Lindenbaum 161k

it looks like you opened the VCF in excel using the tab AND the semicolon as the delimiter.

enter image description here

ADD COMMENT • link 2.5 years ago by Pierre Lindenbaum 161k

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Thank you very much! You are right. And yeah, I should've used R or Python. Thanks.

ADD REPLY • link 2.5 years ago by Camila Martínez ▴ 40