samtools-help

[Samtools-help] Release 1.23.1

Wed, 18 Mar 2026 17:35:43 GMT

2026/03/18 -- Robert Davies

[Samtools-help] Release 1.23

Tue, 16 Dec 2025 15:58:08 GMT

2025/12/16 -- Robert Davies

[Samtools-help] SAMtools and HTSlib release 1.22.1

Mon, 14 Jul 2025 16:10:56 GMT

2025/07/14 -- Robert Davies

[Samtools-help] Release 1.22

Fri, 30 May 2025 14:31:12 GMT

2025/05/30 -- Robert Davies

Re: [Samtools-help] mpileup differences between samtools and bcftools [EXT]

Wed, 30 Oct 2024 17:56:48 GMT

2024/10/30 -- Robert Davies

[Samtools-help] mpileup differences between samtools and bcftools

Mon, 21 Oct 2024 23:35:09 GMT

2024/10/21 -- Nate Brown

[Samtools-help] Release 1.21

Thu, 12 Sep 2024 16:00:33 GMT

2024/09/12 -- Robert Davies

[Samtools-help] Release 1.20

Mon, 15 Apr 2024 17:19:43 GMT

2024/04/15 -- Robert Davies

[Samtools-help] SAMtools release 1.19.2

Wed, 24 Jan 2024 12:43:52 GMT

2024/01/24 -- Robert Davies

[Samtools-help] SAMtools and HTSlib release 1.19.1

Mon, 22 Jan 2024 12:11:23 GMT

2024/01/22 -- Robert Davies

[Samtools-help] Release 1.19

Tue, 12 Dec 2023 16:24:06 GMT

2023/12/12 -- Robert Davies

Re: [Samtools-help] new user

Tue, 24 Oct 2023 16:10:31 GMT

2023/10/24 -- Tom Blackwell

[Samtools-help] new user

Tue, 24 Oct 2023 10:09:58 GMT

2023/10/24 -- Christopher Blair

[Samtools-help] Release 1.18

Tue, 25 Jul 2023 13:15:03 GMT

2023/07/25 -- Robert Davies

Re: [Samtools-help] support to CRAM gzip [EXT]

Wed, 05 Jul 2023 15:05:16 GMT

2023/07/05 -- James Bonfield

[Samtools-help] support to CRAM gzip

Wed, 05 Jul 2023 13:12:51 GMT

2023/07/05 -- Adrian

[Samtools-help] Release 1.17

Tue, 21 Feb 2023 14:40:04 GMT

2023/02/21 -- Robert Davies

[Samtools-help] Problem with RNAME field in bam

Tue, 29 Nov 2022 19:06:08 GMT

2022/11/29 -- gilsanan

[Samtools-help] Samtools installation problem

Wed, 09 Nov 2022 12:29:33 GMT

2022/11/09 -- Trine Riemer

[Samtools-help] Fwd: Humble request and help_replacing variants that failed quality metrics with "N" with bcftools [EXT]

Wed, 02 Nov 2022 09:11:29 GMT

2022/11/02 -- Jennifer Liddle

Re: [Samtools-help] Question about samtools mpileup and overlapping reads [EXT]

Tue, 25 Oct 2022 14:57:17 GMT

2022/10/25 -- James Bonfield

[Samtools-help] Question about samtools mpileup and overlapping reads

Tue, 25 Oct 2022 14:26:23 GMT

2022/10/25 -- Carla Mariner Llicer

Re: [Samtools-help] consensus not recognized [EXT]

Thu, 08 Sep 2022 08:09:01 GMT

2022/09/08 -- James Bonfield

[Samtools-help] SAMtools release 1.16.1

Fri, 02 Sep 2022 14:20:56 GMT

2022/09/02 -- Robert Davies

[Samtools-help] Release 1.16

Thu, 18 Aug 2022 14:18:40 GMT

2022/08/18 -- Robert Davies

Re: [Samtools-help] bcftools isec retain duplicates [EXT]

Thu, 04 Aug 2022 08:20:19 GMT

2022/08/04 -- James Bonfield

Re: [Samtools-help] bcftools isec retain duplicates [EXT]

Thu, 04 Aug 2022 07:45:24 GMT

2022/08/04 -- Thomas Juettemann

Re: [Samtools-help] bcftools isec retain duplicates [EXT]

Wed, 03 Aug 2022 16:51:52 GMT

2022/08/03 -- Robert Davies

[Samtools-help] bcftools isec retain duplicates

Tue, 02 Aug 2022 18:15:49 GMT

2022/08/02 -- Thomas Juettemann

Re: [Samtools-help] questions about samtools index

Fri, 22 Apr 2022 15:12:45 GMT

2022/04/22 -- Peter Cock via Samtools-help

[Samtools-help] questions about samtools index

Thu, 21 Apr 2022 05:39:45 GMT

2022/04/21 -- Ruixue Liu

[Samtools-help] Release 1.15.1

Thu, 07 Apr 2022 16:52:18 GMT

2022/04/07 -- Robert Davies

[Samtools-help] Release 1.15

Mon, 21 Feb 2022 15:15:23 GMT

2022/02/21 -- Robert Davies

Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice [EXT]

Wed, 19 Jan 2022 14:39:51 GMT

2022/01/19 -- Robert Davies

Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice

Wed, 19 Jan 2022 10:10:25 GMT

2022/01/19 -- Sabine van Schie

Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice

Wed, 19 Jan 2022 00:09:36 GMT

2022/01/19 -- Robert Davies

Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice [EXT]

Tue, 18 Jan 2022 18:21:22 GMT

2022/01/18 -- James Bonfield

Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice

Tue, 18 Jan 2022 17:53:36 GMT

2022/01/18 -- Peter Cock via Samtools-help

[Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice

Tue, 18 Jan 2022 17:44:31 GMT

2022/01/18 -- Sabine van Schie

Re: [Samtools-help] changing the order of input changes samtools merge ouput [EXT]

Thu, 13 Jan 2022 09:29:12 GMT

2022/01/13 -- James Bonfield

[Samtools-help] changing the order of input changes samtools merge ouput

Thu, 13 Jan 2022 09:22:58 GMT

2022/01/13 -- Zhezhen Wang

Re: [Samtools-help] bcftools mpileup help [EXT]

Wed, 05 Jan 2022 14:13:36 GMT

2022/01/05 -- Petr Danecek

[Samtools-help] bcftools mpileup help

Tue, 04 Jan 2022 15:15:21 GMT

2022/01/04 -- bparreira

Re: [Samtools-help] Question regarding SAMtools tview alignment characters [EXT]

Tue, 04 Jan 2022 09:51:38 GMT

2022/01/04 -- James Bonfield

[Samtools-help] Question regarding SAMtools tview alignment characters

Tue, 21 Dec 2021 12:56:15 GMT

2021/12/21 -- Loïc Meunier

Re: [Samtools-help] BCF tools 1.9 header order important? [EXT]

Mon, 29 Nov 2021 12:27:23 GMT

2021/11/29 -- Petr Danecek

[Samtools-help] BCF tools 1.9 header order important?

Mon, 29 Nov 2021 09:54:08 GMT

2021/11/29 -- Thomas Juettemann

Re: [Samtools-help] BCF tools sort [EXT]

Tue, 09 Nov 2021 09:08:36 GMT

2021/11/09 -- James Bonfield

[Samtools-help] BCF tools sort

Mon, 08 Nov 2021 16:02:09 GMT

2021/11/08 -- Thomas Juettemann

[Samtools-help] Release 1.14

Fri, 22 Oct 2021 15:09:16 GMT

2021/10/22 -- Robert Davies

[Samtools-help] samtools stats - can I get base frequency based on the position in an alignment rather than original sequence position?

Fri, 24 Sep 2021 08:33:29 GMT

2021/09/24 -- Benjamin Franzmayr

Re: [Samtools-help] Samtools write files to S3 bucket [EXT]

Thu, 16 Sep 2021 07:48:39 GMT

2021/09/16 -- Dilkash Ghazala

Re: [Samtools-help] Samtools write files to S3 bucket [EXT]

Tue, 14 Sep 2021 14:09:39 GMT

2021/09/14 -- Andrew Whitwham

Re: [Samtools-help] Samtools write files to S3 bucket [EXT]

Tue, 14 Sep 2021 14:04:23 GMT

2021/09/14 -- Dilkash Ghazala

Re: [Samtools-help] Samtools write files to S3 bucket [EXT]

Tue, 14 Sep 2021 13:56:32 GMT

2021/09/14 -- Andrew Whitwham

Re: [Samtools-help] Samtools write files to S3 bucket [EXT]

Tue, 14 Sep 2021 10:34:35 GMT

2021/09/14 -- Dilkash Ghazala

Re: [Samtools-help] Samtools write files to S3 bucket [EXT]

Tue, 14 Sep 2021 08:23:37 GMT

2021/09/14 -- Andrew Whitwham

[Samtools-help] Samtools write files to S3 bucket

Mon, 13 Sep 2021 18:17:26 GMT

2021/09/13 -- Dilkash Ghazala

Re: [Samtools-help] Samtools-help Digest, Vol 140, Issue 1

Wed, 25 Aug 2021 14:03:17 GMT

2021/08/25 -- Dr . Frank Vorhölter

Re: [Samtools-help] Samtools-help Digest, Vol 140, Issue 1

Wed, 25 Aug 2021 13:50:36 GMT

2021/08/25 -- Stéphane Plaisance

[Samtools-help] samtools depth multi-threading option

Tue, 24 Aug 2021 14:15:00 GMT

2021/08/24 -- Dr . Frank Vorhölter

Re: [Samtools-help] Different coverage between weeSAM and samtools mpileup result [EXT]

Mon, 26 Jul 2021 08:09:54 GMT

2021/07/26 -- James Bonfield

[Samtools-help] Different coverage between weeSAM and samtools mpileup result

Fri, 23 Jul 2021 18:11:53 GMT

2021/07/23 -- Ching Ching WEE

[Samtools-help] Release 1.13

Fri, 09 Jul 2021 11:23:47 GMT

2021/07/09 -- Robert Davies

Re: [Samtools-help] Samtools Reheader help request [EXT]

Tue, 22 Jun 2021 10:03:02 GMT

2021/06/22 -- Marsha Wallace

Re: [Samtools-help] Samtools Reheader help request [EXT]

Tue, 22 Jun 2021 09:47:19 GMT

2021/06/22 -- Valeriu Ohan

[Samtools-help] Samtools Reheader help request

Thu, 17 Jun 2021 15:09:35 GMT

2021/06/17 -- Marsha Wallace

[Samtools-help] SAM tag for polyA sites

Fri, 16 Apr 2021 07:15:59 GMT

2021/04/16 -- Kodali, Vamsi (NIH/NLM/NCBI) [C] via Samtools-help

[Samtools-help] Release 1.12

Wed, 17 Mar 2021 16:30:17 GMT

2021/03/17 -- Robert Davies

Re: [Samtools-help] fail to read header in v1.10, v1.11 [EXT]

Thu, 11 Mar 2021 10:08:57 GMT

2021/03/11 -- James Bonfield

Re: [Samtools-help] fail to read header in v1.10, v1.11

Thu, 11 Mar 2021 08:51:11 GMT

2021/03/11 -- John Marshall

[Samtools-help] fail to read header in v1.10, v1.11

Thu, 11 Mar 2021 08:33:19 GMT

2021/03/11 -- Remik Ziemlinski

[Samtools-help] samtools mpileup --no-BAQ

Wed, 11 Nov 2020 17:37:25 GMT

2020/11/11 -- Shadrina, Mariya

Re: [Samtools-help] generating headers [EXT]

Wed, 28 Oct 2020 07:22:23 GMT

2020/10/28 -- Valeriu Ohan

[Samtools-help] generating headers

Tue, 27 Oct 2020 22:14:25 GMT

2020/10/27 -- Baiba Alksere

Re: [Samtools-help] tabix and bgzip [EXT]

Mon, 12 Oct 2020 09:13:51 GMT

2020/10/12 -- Andrew Whitwham

[Samtools-help] tabix and bgzip

Mon, 12 Oct 2020 07:26:51 GMT

2020/10/12 -- Baiba Alksere

Re: [Samtools-help] Release 1.11 [EXT]

Thu, 24 Sep 2020 17:02:56 GMT

2020/09/24 -- Elisabeth Diatta via Samtools-help

Re: [Samtools-help] samtools view -L vs location args [EXT]

Thu, 24 Sep 2020 11:45:30 GMT

2020/09/24 -- Keiran Raine

Re: [Samtools-help] samtools view -L vs location args [EXT]

Thu, 24 Sep 2020 11:01:30 GMT

2020/09/24 -- Valeriu Ohan

[Samtools-help] samtools view -L vs location args

Thu, 24 Sep 2020 10:12:40 GMT

2020/09/24 -- Keiran Raine

Re: [Samtools-help] Release 1.11 [EXT]

Thu, 24 Sep 2020 08:33:29 GMT

2020/09/24 -- Petr Danecek

Re: [Samtools-help] Release 1.11 [EXT]

Wed, 23 Sep 2020 22:18:30 GMT

2020/09/23 -- Elisabeth Diatta via Samtools-help

Re: [Samtools-help] Release 1.11 [EXT]

Wed, 23 Sep 2020 06:40:12 GMT

2020/09/23 -- Petr Danecek

Re: [Samtools-help] Release 1.11

Wed, 23 Sep 2020 02:28:53 GMT

2020/09/23 -- Elisabeth Diatta via Samtools-help

[Samtools-help] Release 1.11

Tue, 22 Sep 2020 13:36:30 GMT

2020/09/22 -- Robert Davies

Re: [Samtools-help] Filter on integer tags not working [EXT]

Fri, 11 Sep 2020 17:14:30 GMT

2020/09/11 -- Robert Davies

[Samtools-help] Filter on integer tags not working

Fri, 11 Sep 2020 16:48:15 GMT

2020/09/11 -- Benjamin Audit

Re: [Samtools-help] problems with header [EXT]

Wed, 02 Sep 2020 09:53:02 GMT

2020/09/02 -- Andrew Whitwham

[Samtools-help] problems with header

Wed, 02 Sep 2020 08:26:02 GMT

2020/09/02 -- Baiba Alksere

Re: [Samtools-help] Bcftools call -G [EXT]

Fri, 14 Aug 2020 06:29:56 GMT

2020/08/14 -- Petr Danecek

[Samtools-help] Bcftools call -G

Thu, 13 Aug 2020 21:33:25 GMT

2020/08/13 -- Pooja Singh

Re: [Samtools-help] samtools stats [EXT]

Thu, 16 Jul 2020 11:45:10 GMT

2020/07/16 -- Nadia Baig

Re: [Samtools-help] samtools stats [EXT]

Thu, 16 Jul 2020 11:23:19 GMT

2020/07/16 -- Andrew Whitwham

Re: [Samtools-help] samtools stats [EXT]

Thu, 16 Jul 2020 10:58:48 GMT

2020/07/16 -- Nadia Baig

Re: [Samtools-help] samtools stats [EXT]

Thu, 16 Jul 2020 10:42:43 GMT

2020/07/16 -- Andrew Whitwham

[Samtools-help] samtools stats

Thu, 16 Jul 2020 10:04:48 GMT

2020/07/16 -- Nadia Baig

Re: [Samtools-help] "Use of uninitialized value $l in numeric lt (<)" Error [EXT]

Mon, 06 Jul 2020 07:42:20 GMT

2020/07/06 -- Petr Danecek

[Samtools-help] "Use of uninitialized value $l in numeric lt (<)" Error

Sun, 05 Jul 2020 19:05:19 GMT

2020/07/05 -- White, Noor (NIH/NEI) [F] via Samtools-help

Re: [Samtools-help] Extracting region as fasta

Fri, 19 Jun 2020 14:31:20 GMT

2020/06/19 -- Colin