Issues

• Mark duplicated reads on sorted bam

  GregoryFaust/samblaster#60 · Filter by author Neo-xbx-00 opened on Jan 26, 2026

• de-duplicating a large sam file

  GregoryFaust/samblaster#59 · Filter by author morien opened on Aug 2, 2024
  2

• Can't find first and/or second of pair in sam block of length

  GregoryFaust/samblaster#58 · Filter by author CaroleBelliardo opened on Aug 2, 2023
  2

• Aligning in Biscuit with samblaster and samtools

  GregoryFaust/samblaster#57 · Filter by author KChadwick78 opened on Jul 12, 2023
  1

• Duplicates were removed but log says 0 dups removed

  GregoryFaust/samblaster#55 · Filter by author sehawk opened on Jan 4, 2023
  1

• Please adapt the metrics

  GregoryFaust/samblaster#52 · Filter by author ToVste opened on Jun 7, 2021

• Option to remove split and disc alignments?

  GregoryFaust/samblaster#51 · Filter by author biobenkj opened on May 6, 2021
  1

• Alpine-based docker build fails

  GregoryFaust/samblaster#49 · Filter by author felixfrenkel opened on Nov 17, 2020
  1

• walltime is twice cpu seconds

  GregoryFaust/samblaster#48 · Filter by author jsmedmar opened on Oct 21, 2020
  3

• can samblaster tackle reads with UMI?

  GregoryFaust/samblaster#47 · Filter by author windtalker6 opened on Sep 16, 2020
  1

• Can't find first and/or second of pair error

  GregoryFaust/samblaster#45 · Filter by author dheerajbobbili1988 opened on May 14, 2020
  1

• Support for DT tag to distinguish PCR and optical duplicates

  GregoryFaust/samblaster#38 · Filter by author seboyden opened on Sep 27, 2018
  6

• Filter out soft/hard clipped reads in a pipe SAM -> SAM ?

  GregoryFaust/samblaster#35 · Filter by author tseemann opened on Mar 27, 2018
  5

• Handle chrM discordants differently

  GregoryFaust/samblaster#23 · Filter by author jdidion opened on Jun 27, 2016

• Support for UMIs

  GregoryFaust/samblaster#20 · Filter by author mjafin opened on Apr 25, 2016
  6