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Old 05-17-2018, 04:42 PM   #1
Location: Georgia

Join Date: Apr 2013
Posts: 19
Default 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?
clintp is offline   Reply With Quote

analysis, bcftools, bioinformatic tools, samtools

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