Question: Will random hexamer priming introduce SNP / SNV detection bias?
1
gravatar for CY
3.5 years ago by
CY550
United States
CY550 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!

snp snv next-gen • 691 views
ADD COMMENTlink modified 3.5 years ago by Pierre Lindenbaum133k • written 3.5 years ago by CY550
1

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.

ADD REPLYlink written 3.5 years ago by Istvan Albert ♦♦ 86k

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.

ADD REPLYlink written 3.5 years ago by CY550
2
gravatar for Pierre Lindenbaum
3.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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.

ADD COMMENTlink written 3.5 years ago by Pierre Lindenbaum133k

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?

ADD REPLYlink written 3.5 years ago by CY550
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