Search results

12-fields bedpe file silently breaks pairtopair

Status: Open.

#1140 In arq5x/bedtools2;

· LukaP-BB opened on Jul 15, 2026

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

Status: Open.

#1139 In arq5x/bedtools2;

· tengchn opened on Mar 10, 2026

bedtools skipping lines in VCF input files

Status: Open.

#1138 In arq5x/bedtools2;

· emeralsh-dev opened on Feb 7, 2026

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

Status: Open.

#1137 In arq5x/bedtools2;

· omegahh opened on Jan 14, 2026

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

Status: Open.

#1135 In arq5x/bedtools2;

· vaishnavpvarma opened on Dec 17, 2025

Unexpected intersections produced by bedtools intersect (v2.31.1)

Status: Open.

#1133 In arq5x/bedtools2;

· Bbbbqsh opened on Nov 18, 2025

pairToPair not working in bedtools > 2.27

Status: Open.

#1131 In arq5x/bedtools2;

· bepoli opened on Oct 23, 2025

Unexpected behavior from -noOverlapping option of bedtools shuffle

Status: Open.

#1126 In arq5x/bedtools2;

· cwhelan opened on Jun 17, 2025

unexpected behavior of pairToBed -ispan

Status: Open.

#1125 In arq5x/bedtools2;

· cooketho opened on Jun 4, 2025

bam to bed behavior when supplementary alignments are present

Status: Open.

#1124 In arq5x/bedtools2;

· LinearParadox opened on May 9, 2025

bedtools flank -s not work

Status: Open.

#1123 In arq5x/bedtools2;

· leon945945 opened on Apr 18, 2025

bedtools merge: groupby

Status: Open.

#1122 In arq5x/bedtools2;

· Gri72 opened on Mar 29, 2025