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postalt.js MAPQ 0 on both chr17 and Alternate Contigs

Open DarioS opened this issue 3 years ago • 1 comments

I have been examining some strange copy number results for the gene KANSL, which is on chr17, chr17_KI270908v1_alt and chr17_GL000258v2_alt. It turns out that almost all of the reads mapping to exons of the gene have MAPQ of 0 on both the primary chromosome, as well as the alternate contig(s). 100% sequence match to all three contigs. Bug?

DarioS avatar Feb 18 '22 06:02 DarioS

Related question: Does anyone use bwa-postalt.js in a production environment? We have been using it for cancer genomics with the aim of reporting results to cancer patients' doctors and running into issues with downstream analyses.

DarioS avatar Feb 22 '22 06:02 DarioS