Question: Will random hexamer priming introduce SNP / SNV detection bias?
1
gravatar for CY
6 months ago by
CY80
United States
CY80 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 • 278 views
ADD COMMENTlink modified 6 months ago by Pierre Lindenbaum103k • written 6 months ago by CY80
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 6 months ago by Istvan Albert ♦♦ 75k

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 5 months ago by CY80
2
gravatar for Pierre Lindenbaum
6 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum103k 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 6 months ago by Pierre Lindenbaum103k

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 6 months ago by CY80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1325 users visited in the last hour