filter for format field using ALT column

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
35/100
Issue type
Documentation
Clarity
Needs clarification
Activity status
Stale
Tech stack
shell
Domain
cli, data

Research direction

Start with the bcftools view expression in the report and the ALT and FORMAT fields it references. Check the expression documentation or implementation to determine whether ALT can select the matching FORMAT value; done means a concise, validated command or a documented limitation.

Written by the indexing model from the issue text.

Description

I have a VCF file with the following FORMAT fields: AU, TU, GU, and CU. I want to calculate the Allele Frequency (AF) for each variant based on the ALT allele and then filter variants where the AF exceeds a threshold of 0.1. The formula for AF is as follows:

AF = \frac{[ALT]U}{(AU + TU + GU + CU)}

I am having difficulty obtaining the ALT count from the ALT field. Currently, I'm achieving this by using the following bcftools view expression:

bcftools view -i '( ALT=="A" & (AU/(AU + TU + GU + TU) > 0.1) ) | ( ALT=="T" & (TU/(AU + TU + GU + TU) > 0.1) ) ' sample_vcf

The expression above is becoming quite lengthy. I'm wondering if there's an alternative approach to achieve the same result.

Thank you,
-Arijit

Dominant language
C
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Forks
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Avg merge
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Merged PRs (30d)
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