github broadinstitute/picard 2.9.4
on GitHub

Bug fix

  • Fix bug in CollectAlignmentSummaryMetrics when paired end alignment data includes single ended (SE) alignments that caused the tool to error (#838; PO-8928). Instead of calculating metrics for PF_READS_IMPROPER_PAIRS on alignments lacking the 0x2 SAM flag (not proper pair), the tool now requires the alignment to (i) be paired (0x1 SAM flag) and (ii) not be in a proper pair (lacks 0x2 SAM flag) for calculating PF_READS_IMPROPER_PAIRS. This results in the tool excluding SE alignments from the calculation given they will lack the 0x1 SAM flag (not paired) and to run successfully. For an introduction to SAM flags, see this blogpost.
3 years ago