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filter VCF based on info field that has a key but no value

I have some INFO fields that look like this:

##INFO=<ID=AF,Number=1,Type=Float,Description="Estimated Alternate Allele Frequency">
##INFO=<ID=MAF,Number=1,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy (R-square)">
##INFO=<ID=ER2,Number=1,Type=Float,Description="Empirical (Leave-One-Out) R-square (available only for genotyped variants)">
##INFO=<ID=IMPUTED,Number=0,Type=Flag,Description="Marker was imputed but NOT genotyped">
##INFO=<ID=TYPED,Number=0,Type=Flag,Description="Marker was genotyped AND imputed">
##INFO=<ID=TYPED_ONLY,Number=0,Type=Flag,Description="Marker was genotyped but NOT imputed">

I understand that if I wanted to filter based on an INFO col key-value pair I could go:

bcftools view -e 'R2<0.9' my_fav.vcf.gz

The IMPUTED, TYPED, TYPED_ONLY keys appear in the info field with no corresponding value, for example:

AF=0.00016;MAF=0.03036;R2=0.13409;IMPUTED

is a complete info field.

Is there a way one could filter TYPED vs IMPUTED variants by using bcftools utility. I know I could probably grep my way through this if need be.

bcftools vcf
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updated by caro1002 • caro1002 • written by curious curious

Interesting question! Can you try if an aggregate function (such as COUNT(IMPUTED)>0) picks up these entries?

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written by Ram Ram 
COUNT() can be applied only on FORMAT fields

it seems :(. . This valueless key is a standard output of Minimac imputation software, I wish it was a value of some key though

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written by curious curious

Have you tried:

bcftools view -e 'IMPUTED' my_fav.vcf.gz

or

bcftools view -i 'IMPUTED' my_fav.vcf.gz

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written by FGV FGV

This was the first thing I tried before posting. when it did not work I was basically stuck because I couldn't see how to do it outside of bcftools. I just like using bcftools because it helps me catch corrupted VCFs sometimes

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written by curious curious

1 answer

You can use the expression =1 (or 0) to test the presence (or absence) of a flag. For example, the following expressions will exclude all imputed SNPs

bcftools view -e 'INFO/IMPUTED=1' or bcftools view -i 'INFO/IMPUTED=0'

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written by caro1002 • caro1002

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