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bcftools - retain low quality read position support?

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  • bcftools - retain low quality read position support?

    Is it possible to have `bcftools call -c` output a DP4 values that add up to the total DP value. I want to call simple consensus sequences based on a basic vote.

    For example, at one position in my VCF file, I have:
    DP=16092 and DP4=74,48,24,600 (alt allele should win 624 to 122)
    Those dont come close to adding up.
    Checking out the position in IGV, the ref allele wins 11355 to 3716.

    I did run samtools mpileup -B to turn off BAQ scoring.
    What am I missing here?
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