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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...