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Understanding implications of DP4/Strand Bias in Bacterial VCF files

Hi,

I'm sorting through some bacterial VCF files generated by bowtie/samtools and a lot of variants have DP4 values indicating the alternative is only on one strand (e.g. DP4 = 5,0,7,0).

The sequences are high-coverage Illumina data.

Is this likely to be sequencing error due to phasing/prephasing rather than a genuine mutation, or could it be strand bias?

Other called variants also yield hits on both strands but do not equal DP (meaning some bases are below the quality threshold); e.g. DP=360, DP4=118,52,54,23 - are these variants likely error?

Thanks!

vcf snp dp4 strand bias filtering
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updated by Kevin Blighe Kevin Blighe • written by f2369583 • f2369583

1 answer

Just looking at the 2 examples that you've mentioned, there looks to be strand bias. The read-depth in the first example is very low, though. There could be various things that could result in strand bias, such as:

You should have an associated P value that indicates strand bias. Also, the information that you've provided should be taken in the context of all other QC information about the data and run before arriving at a decision.

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written by Kevin Blighe Kevin Blighe

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