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Installation fails - configure: error: cannot find required auxiliary files: config.guess config.sub

Status: Open.

#2299 In samtools/samtools;

· pierfrancescomartinello opened on Jan 22, 2026

-T (--reference) parameter for samtools reset

Status: Open.

#2297 In samtools/samtools;

· ryansohny opened on Jan 18, 2026

samtools markdup memory usage on high-depth regions

Status: Open.

#2296 In samtools/samtools;

· daviesrob opened on Jan 15, 2026

mpileup on extremely high depth region

Status: Open.

#2293 In samtools/samtools;

· gevro opened on Jan 2, 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

Max depth for samtools consensus

Status: Open.

#2238 In samtools/samtools;

· ammaraziz opened on Jul 15, 2025

BED-filtering and non-primary alignments

Status: Open.

#2232 In samtools/samtools;

· sjaenick opened on Jun 26, 2025

mpileup: Question on null read selection during overlap tweaking with respect to deletions

Status: Open.

#2228 In samtools/samtools;

· epiliper opened on Jun 10, 2025