List view

easy way to modify qname?

Status: Open.

#1090 In samtools/samtools;

· brianjohnhaas opened on Aug 20, 2019

Shift reads in sam/bam files directly

enhancement

Status: Open.

#868 In samtools/samtools;

· AidanQuinn opened on Jun 11, 2018

Reheader: update existing index

Status: Open.

#643 In samtools/samtools;

· eroller opened on Feb 23, 2017

samtools fastq invalid result

Status: Open.

#634 In samtools/samtools;

· keiranmraine opened on Feb 8, 2017

Add "-v" (invert selection) to "samtools faidx file.fa <regions>" ?

Status: Open.

#553 In samtools/samtools;

· tseemann opened on Apr 5, 2016

Header merging does not merge @HD headers

Status: Open.

#390 In samtools/samtools;

· jmarshall opened on May 12, 2015

add option -t for turning off translation; add option -p and -i for samtools merge

Status: Open (in progress).

samtools/samtoolsnumber 369

#369 In samtools/samtools;

· ionzhangj8 opened on Mar 25, 2015

-l option in mpileup doesn't use the bam index

D2: Moderate

P1: Urgent

Status: Open.

#329 In samtools/samtools;

· jeanlain opened on Dec 8, 2014

fixmates doesn't cope with more than 2 primary read aligments.

Status: Open.

#310 In samtools/samtools;

· jkbonfield opened on Oct 22, 2014

Merge should check for equivalent chromosomes in files to be merged

enhancement

Status: Open.

#207 In samtools/samtools;

· jmarshall opened on Apr 24, 2014

Reference sequence name ambiguities.

Status: Open.

#149 In samtools/samtools;

· jkbonfield opened on Feb 17, 2014

mpileup -C option documentation is misleading, but I'm not sure it could be documented correctly short of a huge wadge of code.

Status: Open.

#124 In samtools/samtools;

· jkbonfield opened on Feb 7, 2014

Samtools view -x / -X don't work as advertised

P3: Low priority

Status: Open.

#120 In samtools/samtools;

· daviesrob opened on Feb 6, 2014

Some indels in homopolymer runs not called with default parameters

D1: Difficult

P2: Desirable

Status: Open.

#117 In samtools/samtools;

· pd3 opened on Jan 29, 2014

samtools view -t to replace the SAM header

D1: Difficult

P2: Desirable

Status: Open.

#80 In samtools/samtools;

· sjackman opened on Oct 22, 2013

query read properties

Status: Open.

#1546 In samtools/samtools;

· robmaz opened on Nov 19, 2021

Bit for bit recovery of original fastq files

Status: Open.

#1928 In samtools/samtools;

· hallundbaek opened on Oct 19, 2023

samtools merge single file too slow.

Status: Open.

#2145 In samtools/samtools;

· y9c opened on Nov 20, 2024

samtools reheader error

Status: Open.

#2157 In samtools/samtools;

· C-YONG opened on Dec 5, 2024

samtools markdup: move UMI from read name to RX tag

Status: Open.

#2181 In samtools/samtools;

· matthdsm opened on Feb 4, 2025

adapter marking and clipping

Status: Open.

#2194 In samtools/samtools;

· dkj opened on Feb 27, 2025