Will random hexamer priming introduce SNP / SNV detection bias?

Question

[CY]

Certain hexamer primers are favored during PCR step and this will cause allele frequency bias in the alignment. I image this bias will affect SNP /SNV calling. Are there any tools correcting this kind of bias? Any comments are appreciated!

[Istvan Albert]

I think that hexamer priming bias is a concern primarily when one needs to compare the coverage changes between different regions of a genome. For example when comparing the levels of two transcripts.

[CY]

You are right. A second thought of this bias: This will not cause bias in SNP / SNV calling right? Although it uneven reads coverage. The allele frequency will not be changed by this.

Answer 1

[Pierre Lindenbaum]

GATK hapcaller inserts the HomopolymerRun annotation in the VCF:

##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">

one can use this annotation during the VariantRecalibration step.

[CY]

A second thought of this bias: This will not cause bias in SNP / SNV calling right? Although it uneven reads coverage. The allele frequency will not be changed by this. Am I right?