How do I use vcftools to filter by variant ID OR variant position?

Question

[jwhite007]

I'm having a problem obtaining a recoded vcf which contains variants with their IDs in a "snp file" OR their positions in a "position file." The following gives only variants with their IDs in the "snp file" AND their positions in the "position file."

vcftools --vcf <input vcf file> --snps <variant IDs file> --positions <variant positions file> --recode --out <output vcf file>

Is there any way that I can obtain that which I desire without having to do each separately, concatenating, and then getting rid of duplicates?

Thanks in advance.

[ATpoint]

Please use the format bar to indicate code. I did it for you this time.

Answer 1

[Pierre Lindenbaum]

not vcftools

using vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html

[jwhite007]

Pierre,

I just realized that you are the creator of jvarkit. Thank you for your hard work in getting that code going and making it freely available and open source.

Cheers, James

[jwhite007]

Pierre,

I'd definitely like this in an easy-to-use tool like vcftools or bcftools, but what you've provided seems to work. Thank you for posting this. I will interrogate further later, however...

vcftools --vcf <input vcf file> --snps <variant IDs file> --recode --out <output vcf file>

gives 1695 variants

vcftools --vcf <input vcf file> --positions <variant positions file> --recode --out <output vcf file>

gives 483 variants

vcftools --vcf <input vcf file> --snps <variant IDs file> --positions <variant positions file> --recode --out <output vcf file>

gives 60 variants

java -jar dist/vcffilterjdk.jar --body -f biostar347173.code <input vcf file> > <output vcf file>

gives 2118 variants

1695 + 483 - 60 = 2118 = Yay!!

[Pierre Lindenbaum]

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