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).
Setting genotypes to missing for certain positions in vcf file
Hi,
Is there a way to set genotypes to missing for a list of positions using vcftools? Thanks!
Best,
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Pierre Lindenbaum
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jtull •
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jtull •
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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.
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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.
split the vcf in two regions , fix the genotypes of one vcf, merge both vcfs.
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see also: How can I convert heterozygous genotype data to missing data?