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Feature Request: Option to strip UR tags from CRAM @SQ header lines

Status: Open.

#2327 In samtools/samtools;

· fplazaonate opened on Apr 21, 2026

is samtools fixmate plus sort equivalent to picard FixMateInformation ?

Status: Open.

#2324 In samtools/samtools;

· BiotechPedro opened on Apr 16, 2026

samtools checksum fails to merge checksums created with --bamseqchksum

Status: Open.

#2323 In samtools/samtools;

· kjsanger opened on Apr 16, 2026

Diff / patch like program for efficient storage of raw + processed data

Status: Open.

#2318 In samtools/samtools;

· daviesrob opened on Mar 26, 2026

cannot specify single read for casava fastq import

Status: Open.

#2307 In samtools/samtools;

· dkj opened on Feb 14, 2026

How "bases mapped (cigar)" value in samtools stats is calculated?

Status: Open.

#2302 In samtools/samtools;

· YuanTian1991 opened on Feb 5, 2026

samtools markdup memory usage on high-depth regions

Status: Open.

#2296 In samtools/samtools;

· daviesrob opened on Jan 15, 2026

samtools faidx - extract a slice of records by index

Status: Open.

#2278 In samtools/samtools;

· prototaxites opened on Oct 17, 2025

Duplicate tags are incorrectly ignored in SAM v1.6 files

Status: Open.

#2272 In samtools/samtools;

· twrightsman opened on Oct 10, 2025

samtools.org security issue?

Status: Open.

#2260 In samtools/samtools;

· faulk-lab opened on Sep 14, 2025

Transparency of sort order tag of collate differs from sort -n

Status: Open.

#2252 In samtools/samtools;

· ASLeonard opened on Aug 21, 2025

Add a collate option to samtools fastq

Status: Open.

#2240 In samtools/samtools;

· daviesrob opened on Jul 24, 2025