set GT values to missing in VCF file for specific sample-variant combinations - bcftools?

Question

[karen2]

Hi - I have a multi-subject vcf file and would like to set specific genotypes (GT) to missing for a set of subjects. However, the subjects that I need to set to missing are different for each variant.

For example, suppose I have this:

CHROM POS ID FORMAT sub1 sub2 sub3

22 12345 rs1111 GT 0/0 0/1 0/1

22 67891 rs2222 GT 1/1 0/0 0/0

22 45678 rs3333 GT 0/0 0/0 0/0

22 34567 rs4444 GT 0/1 0/0 0/1

I want to set rs1111 to missing for sub1, but then set rs3333 to missing for sub2 and sub3, so my results would look like this:

CHROM POS ID FORMAT sub1 sub2 sub3

22 12345 rs1111 GT ./. 0/1 0/1

22 67891 rs2222 GT 1/1 0/0 0/0

22 45678 rs3333 GT 0/0 ./. ./.

22 34567 rs4444 GT 0/1 0/0 0/1

I prefer using bcftools or vcftools, but am open to other ideas!

Answer 1

[Pierre Lindenbaum]

using vcffilterjdk https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ , for your first rs, not tested.

 java -jar  varkit.jar vcffilterjdk -e 'if("rs3333".equals(variant.getID())) {return new VariantContextBuilder(variant).genotypes(variant.getGenotypes().stream().map(G->(G.getSampleName().equals("sub2") || G.getSampleName().equals("sub3"))?GenotypeBuilder.createMissing(G.getSampleName(),G.getPloidy()):G ).collect(Collectors.toList())).make();} return variant;'  input.vcf

[karen2]

Wow, thanks! It took me a few days to get this installed and running, but it is doing something close to what I need now. Thank you so much!

I am not very famil1ar with java, so I hope you don't mind me asking a couple follow up questions:

1. So in my 'real life' VCF, I have other fields in FORMAT besides GT. For example, I have GT:GQ:SQ:DP:CN. I would like only the GT column to be set to ./. but the other format fields to remain the same. Right now, all fields are being set to missing. For example, I would like 0/0:51:0:57:2 to be changed only to ./.:51:0:57:2 instead of ./.:.:.:.. I assume something in the java expression needs to change, but I am not sure what.

2. In my 'real life' VCF, I have about ~500 variants that each need to be set to missing for between 1-20 subjects. I could use your command ~500 times, each time creating a new output VCF, but I wonder if there is a way to do all of this in the same run of vcffilterjdk without having just an extremely long -e command. Any thoughts?

Again, thanks very much for your help!