Issues

• bedtools intersect --split -r -f drops or wrongly accepts pairs when more than one -b record overlaps the same -a record

  arq5x/bedtools2#1142 · Filter by author aerusakovich opened on Aug 5, 2026
  1

• Intersect fails to find any hits when the target has splice variants and both "-split" and "-wao -f" are used

  arq5x/bedtools2#1141 · Filter by author jlparmley opened on Jul 27, 2026
  2

• 12-fields bedpe file silently breaks pairtopair

  arq5x/bedtools2#1140 · Filter by author LukaP-BB opened on Jul 15, 2026

• Possible multiinter inconsistency with large BED collections: interval reported as 0 despite direct overlap

  arq5x/bedtools2#1139 · Filter by author tengchn opened on Mar 10, 2026

• bedtools skipping lines in VCF input files

  arq5x/bedtools2#1138 · Filter by author emeralsh-dev opened on Feb 7, 2026

• bedtools fails to read CRAM 3.1 files produced by HTSlib ≥1.22

  arq5x/bedtools2#1137 · Filter by author omegahh opened on Jan 14, 2026

• How to Annotate Gene names in *.bedmethyl files generated from ModKit?

  arq5x/bedtools2#1135 · Filter by author vaishnavpvarma opened on Dec 17, 2025

• Unexpected intersections produced by bedtools intersect (v2.31.1)

  arq5x/bedtools2#1133 · Filter by author Bbbbqsh opened on Nov 18, 2025

• pairToPair not working in bedtools > 2.27

  arq5x/bedtools2#1131 · Filter by author bepoli opened on Oct 23, 2025

• Unexpected behavior from -noOverlapping option of bedtools shuffle

  arq5x/bedtools2#1126 · Filter by author cwhelan opened on Jun 17, 2025

• unexpected behavior of pairToBed -ispan

  arq5x/bedtools2#1125 · Filter by author cooketho opened on Jun 4, 2025

• bam to bed behavior when supplementary alignments are present

  arq5x/bedtools2#1124 · Filter by author LinearParadox opened on May 9, 2025

• bedtools flank -s not work

  arq5x/bedtools2#1123 · Filter by author leon945945 opened on Apr 18, 2025
  1

• bedtools merge: groupby

  arq5x/bedtools2#1122 · Filter by author Gri72 opened on Mar 29, 2025

• null-pointer-dereference

  arq5x/bedtools2#1121 · Filter by author QiuYitai opened on Mar 25, 2025

• bedtools maskfasta with incomplete chromosomes

  arq5x/bedtools2#1118 · Filter by author r-poloni opened on Feb 18, 2025

• Feature request: only check first column of genome file for -g option of bedtools intersect

  arq5x/bedtools2#1117 · Filter by author bentyeh opened on Feb 8, 2025

• Feature request: remove need to supply genome file to bedtools intersect -sorted when the inputs are already chromosome-grouped and coordinate-sorted.

  arq5x/bedtools2#1116 · Filter by author bentyeh opened on Feb 8, 2025

• unionbedg -header not working

  arq5x/bedtools2#1114 · Filter by author GregorD96 opened on Jan 29, 2025
  1

• Bedtools runs infinitely with large memory usage under sorted option when there's unmapped reads

  arq5x/bedtools2#1113 · Filter by author kheber opened on Jan 22, 2025

• bedtools intersect with -g option: chromosomes without regions cause intersections being missed

  arq5x/bedtools2#1111 · Filter by author ChrissiKalk97 opened on Jan 9, 2025

• static.binary missing for 2.31.1

  arq5x/bedtools2#1110 · Filter by author bartcharbon opened on Dec 16, 2024

• Inconsistent naming convention warning

  arq5x/bedtools2#1109 · Filter by author fa8sanger opened on Nov 28, 2024

• Bedtools Genomecov -pc Option: Name-Sorted BAM File Error in Version 2.31.0

  arq5x/bedtools2#1108 · Filter by author yeeun3712 opened on Nov 14, 2024

• CLI seg faults

  arq5x/bedtools2#1106 · Filter by author zeeev opened on Oct 29, 2024