bcftools can not call low allele frequency

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#1,707 5 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start by reproducing the reported samtools mpileup | bcftools -vm pipeline and inspect how the DP4 frequency is calculated from its output. Read the bcftools calling and filtering documentation or entry points to determine whether a default frequency filter is involved. Done would require explaining the observed cutoff and identifying how variants below 20% can be retained.

Written by the indexing model from the issue text.

Description

Hello there, I'm doing some SNP calling with samtools mpileup -Q 0 -uvf | bcftools -vm -Oz
but after running the pipeline, I noticed that all my SNPs are with frequencies above 20% (calculate using (DP4[3]+DP4[2]) /(DP4[3]+DP4[2]+DP4[1]+DP4[0]). I don't know why. Is there a default paremeter for control the frequency filltering ??? How can I get the rest one (<20%)???
Hope for help!!! Thanks!!!

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