Question: How Large Can A Coverage Discrepancy Be Between Two Aligners, Specifically Bwa And Novoalign
3
gravatar for Matt Miossec
7.7 years ago by
Matt Miossec350
UK/Oxford/Wellcome Centre for human genetics
Matt Miossec350 wrote:

I am involved in a project where variants have been called using two different aligner/variant caller pipelines on the same illumina sequenced data and we have found that there are some major discrepancies in reported coverage for some of the positions in which variants have been found. While I expect there to be some difference in coverage between two aligners, am I right to suspect that 50+ difference in coverage is uncommon or simply not possible? The aligners used are well established ones: BWA and Novoalign.

alignment bwa • 1.8k views
ADD COMMENTlink modified 7.5 years ago by Jeremy Leipzig19k • written 7.7 years ago by Matt Miossec350
3

You should check (and if you wish, post) alignment parameters. Maybe one of the two software was used with stricter parameters? In my experience, the two aligners usually give similar results. Also, check your average coverage : if your coverage is 1000 becaues you are doing resequencing of a small target then a 50+ difference is not so great.

ADD REPLYlink written 7.7 years ago by Fabio Marroni2.7k
1
gravatar for Jeremy Leipzig
7.5 years ago by
Philadelphia, PA
Jeremy Leipzig19k wrote:

Do your total counts resemble the ones below?

enter image description here

ADD COMMENTlink written 7.5 years ago by Jeremy Leipzig19k

Thanks, I'll check.

ADD REPLYlink written 7.5 years ago by Matt Miossec350
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