VCFtools no vcf output

Question

[Julian.dekker]

Hi All,

I am very confused using vcftools.

vcftools --gzvcf $data_loc/chr10.dose.vcf.gz --snps chr10-snpIDs-tmp.txt --recode --out chr10.filter

outputs right, but I need the information in the info field so I tried using.

vcftools --gzvcf $data_loc/chr10.dose.vcf.gz --snps chr10-snpIDs-tmp.txt --recode-INFO-all --out chr10.filter

When I run the bottom command it will generate a .info file but not the VCF itself. What am I doing wrong?

Kind regards,

Julian

Answer 1

[Ram]

Please read the documentation. You need both --recode and --recode-INFO-all/--recode-info.

Pro-tip: Switch to bcftools. It's much better than bcftools. The very fact that you need to ask vcftools to output vcf after a filter operation makes it an unintuitive (to put it mildly) tool.

[Julian.dekker]

Thank you, I had assumed recode-INFO-all was the same as recode but with INFO. very unintuitive for sure, I will check out bcftools.

[Ram]

It's a bad tool. Plus, it's outdated almost to the extent of becoming abandonware. The last proper vcftools release was in 2018, and the last commit happened 2 years ago. As for bcftools, the last release was 25 days ago and the last commit happened hours ago.

[Ram]

Please accept my answer to mark the post as solved.