Warning: Expected at least 2 parts in FORMAT entry: ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1">

Question

[juan.sainz]

Hi guys,

I am trying to remove indels from my GWAS using vcftools and I got an error.

VCFtools - 0.1.16
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --vcf All_chr_merged
    --recode-INFO-all
    --out All_chr_merged_withoutindels
    --recode
    --remove-indels

Warning: Expected at least 2 parts in FORMAT entry: ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1">
After filtering, kept 532 out of 532 Individuals

Could you please help me to solve this issue?

Thanks in advance!

[GenoMax]

Please edit the post and consider using a concise title. Posting "warning" (in this case) in title is not productive. It does not tell people about which program you are trying to use and for what.

Answer 1

[Pierre Lindenbaum]

I got an error

Warning: Expected at least 2 parts in FORMAT entry: ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1">

I don't see an error, just a warning. https://github.com/vcftools/vcftools/issues/134#issuecomment-496640699

It's just a warning that vcftools doesn't know how to handle the comma within the Description tag. If you remove that comma in the description, the warning will go away. Otherwise, it can generally be ignored.

Furthermore vctools is deprecated, use bcftools

bcftools view --exclude-types indels -O z -o out.vcf.gz in.vcf