Setting genotypes to missing for certain positions in vcf file

Question

[jtull]

Hi,

Is there a way to set genotypes to missing for a list of positions using vcftools? Thanks!

Best,

[Pierre Lindenbaum]

see also: How can I convert heterozygous genotype data to missing data?

Answer 1

[Pierre Lindenbaum]

bcftools plugin setGT : https://samtools.github.io/bcftools/howtos/plugins.html

Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.

[jtull]

Thanks for your answer, however, these solutions all seem to rely on the info in other columns. What I want to do is to set certain genotypes to missing based solely on their position because I have a list positions (that I created using info that isn't in the other columns).

[jtull]

So, for instance, I have a file called X.pos that includes positions to be set to missing, it looks like below: head X.pos: 18863 34659 47022 61505 ... (each pos is a separate line)

In this link http://samtools.github.io/bcftools/bcftools.html, I saw that ID=@file selects the lines with ID present in the file and with similar logic I tried the following to filter the positions in the file:

bcftools filter -e 'POS=@X.pos' my.vcf.gz

It is just to see if I can filter the vcf to only include the positions in the file but no luck so far. I know the number of positions in X.pos and the output generated is far larger, so I am making a mistake somewhere. maybe the X.pos format is wrong? Any idea?

If It it worked, I was going to try setGT.

[Pierre Lindenbaum]

split the vcf in two regions , fix the genotypes of one vcf, merge both vcfs.

[jtull]

Solved it with python, thanks!