I am hoping to estimate the proportion of mismatches, insertions, and deletions to a reference sequence in a BAM file. I applied the picard CollectAlignmentSummaryMetrics tool, and I find that all of my reads pass filtering, 2477324592 total bases are aligned, and I have a PF_MISMATCH_RATE of 0.000348. However, when I instead sum all of the "NM" tags for all alignments, then divide by the total number of aligned bases, I calculate a higher mismatch rate of 0.0008732263. I similarly overestimate if I try to get the total number of indels from the MD tags, then compare to PF_INDEL_RATE. Could someone explain the discrepancy here? Thanks for your help.
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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
