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Will random hexamer priming introduce SNP / SNV detection bias?

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!

next-gen snp snv
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by CY CY

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.

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written by Istvan Albert Istvan Albert

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.

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written by CY CY

1 answer

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.

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written by Pierre Lindenbaum Pierre Lindenbaum

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?

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written by CY CY

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