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.
Question: How Large Can A Coverage Discrepancy Be Between Two Aligners, Specifically Bwa And Novoalign
7.7 years ago by
Matt Miossec • 350
UK/Oxford/Wellcome Centre for human genetics
Matt Miossec • 350 wrote:
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