Question: Will random hexamer priming introduce SNP / SNV detection bias?
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CY • 100 wrote:
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!
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modified 8 months ago
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Pierre Lindenbaum ♦ 106k
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8 months ago by
CY • 100
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.
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.