SNV occuring 2 fold more in forward than in reverse reads should be filtered?
0
0
Entering edit mode
8 months ago
jeni ▴ 60

Hi!

I am reviewing the SNVs of a vcf in IGV. I have seen that some of them occurs almost 2 fold in forward than in reverse reads (or viceversa) of a gene panel deep sequencing bam.

As an example: I have an SNV (G>T) supported by 795 forward reads and 496 reverse reads. The reference allele is supported, however, by 6677 forward reads and 6716 reverse reads. I know that a clear bias by strand is indicative of a sequencing error, so I was wondering if I should consider as a bias the support of the variant allele, and therefore, if I should filter it.

Thanks!

VariantCalling • 176 views
ADD COMMENT

Login before adding your answer.

Traffic: 857 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6