Issues

• Add opt-in stderr progress flag for per-chromosome progress events

  brentp/mosdepth#269 · Filter by author carstenerickson opened on May 15, 2026

• CRAM 3.1 slice decode failure in mosdepth v0.3.14 with bundled/static htslib

  brentp/mosdepth#268 · Filter by author grahamlbanes opened on May 5, 2026
  2

• Error processing BAM file generated by bwa-mem2

  brentp/mosdepth#259 · Filter by author Hoeze opened on Nov 19, 2025
  13

• Bug: Incorrect output v 0.3.10 in coverage of d4 vs summary.txt

  brentp/mosdepth#254 · Filter by author peterpru opened on Sep 12, 2025
  10

• --d4 missing from v0.3.11 from conda

  brentp/mosdepth#251 · Filter by author cademirch opened on Jul 15, 2025
  5

• How to use --d4?

  brentp/mosdepth#247 · Filter by author LudvigOlsen opened on Jan 17, 2025
  5

• Mosdepth fails when run with less than 8GB RAM on ~50MB CRAM

  brentp/mosdepth#245 · Filter by author dennishendriksen opened on Dec 9, 2024
  21

• Median is Only for Histogram

  brentp/mosdepth#242 · Filter by author DarioS opened on Nov 20, 2024

• v3.9.0 not available via quay.io

  brentp/mosdepth#240 · Filter by author bartcharbon opened on Nov 14, 2024
  1

• Differences in WES Coverage Values (Mosdepth Versions 0.3.3 and 0.3.8)

  brentp/mosdepth#234 · Filter by author niyati1211 opened on Jun 13, 2024
  2

• : in region strings passed to --chrom

  brentp/mosdepth#230 · Filter by author julibeg opened on Apr 22, 2024

• addition of min and max counts to prefix.regions.bed.gz

  brentp/mosdepth#226 · Filter by author joelarkman opened on Apr 9, 2024

• [question]: mosdepth 0.3.7 via bioconda/docker

  brentp/mosdepth#225 · Filter by author tamuanand opened on Mar 21, 2024

• Warnings about invalid chromosome intervals .

  brentp/mosdepth#223 · Filter by author Heather1999 opened on Feb 18, 2024
  1

• Report all chromosomes/regions even though they have zero coverage

  brentp/mosdepth#222 · Filter by author xsoleacha opened on Feb 12, 2024
  2

• Summary output with --use-median

  brentp/mosdepth#220 · Filter by author Adamtaranto opened on Jan 17, 2024
  2

• [Question]: mosdepth 0.3.4 via Docker or Conda

  brentp/mosdepth#204 · Filter by author tamuanand opened on Jul 27, 2023
  2

• misleading output in summary.txt file

  brentp/mosdepth#198 · Filter by author nservant opened on Mar 24, 2023
  3

• .mosdepth.region.dist.txt missing values?

  brentp/mosdepth#190 · Filter by author adamrtalbot opened on Dec 6, 2022

• In summary.txt what's the difference between length and bases?

  brentp/mosdepth#188 · Filter by author nuno5645 opened on Nov 21, 2022

• Percentage of Coverage for Exome Bed file

  brentp/mosdepth#186 · Filter by author kiranpatil222 opened on Oct 13, 2022
  1

• Coverage by region vs. Global dist

  brentp/mosdepth#184 · Filter by author hlfreund opened on Oct 10, 2022
  8

• Optionally report uncovered contigs in summary file

  brentp/mosdepth#180 · Filter by author dpryan79 opened on Aug 3, 2022
  

• plot.dist.py output to screen only

  brentp/mosdepth#178 · Filter by author space-beaver opened on Jul 1, 2022
  4

• threshold output to indicate how many bases in each region are covered at the given thresholds.

  brentp/mosdepth#176 · Filter by author asmlgkj opened on Apr 25, 2022