sambamba-discussion

1–28 of 28

Here we have discussions on sambamba that are not related to direct bugs in the code base. For those, use https://github.com/biod/sambamba/issues.

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Ricardo Linares

Jan 4

Filtering out chromosomes still leave empty records in header

I filter out unwanted chromosomes or assemblies using: sambamba view -f bam -F "ref_name =~ /^

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Filtering out chromosomes still leave empty records in header

I filter out unwanted chromosomes or assemblies using: sambamba view -f bam -F "ref_name =~ /^

Jan 4

Theo Allnutt

7/24/23

Where is the current release? The link only shows source code.

Link only shows source: https://github.com/biod/sambamba/releases

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Where is the current release? The link only shows source code.

Link only shows source: https://github.com/biod/sambamba/releases

7/24/23

Sven Winter

5/23/23

Sambamba depth base does not accurately list depth per base in output

Hi, I have tried several older and newer versions of Sambamba but for whatever reason my output list

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Sambamba depth base does not accurately list depth per base in output

Hi, I have tried several older and newer versions of Sambamba but for whatever reason my output list

5/23/23

Christopher Husted

5/3/23

Benchmark relative to Picard MarkDuplicates

Hi there, I was wondering if you could provide more detail about the speed increases relative to

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Benchmark relative to Picard MarkDuplicates

Hi there, I was wondering if you could provide more detail about the speed increases relative to

5/3/23

Maxine Liu, Nick Rozinsky3

7/21/22

sambamba-sort error: index exceeds array of length

There is probably no support for csi index. However I think that index may be not necessary for

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sambamba-sort error: index exceeds array of length

There is probably no support for csi index. However I think that index may be not necessary for

7/21/22

Vamsi Kodali

9/9/21

Using CSI index

I work with genomes with chromosomes that are >512Mbp in size. When generating BAM index file

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Using CSI index

I work with genomes with chromosomes that are >512Mbp in size. When generating BAM index file

9/9/21

Jordi Camps, Pjotr Prins3

8/17/21

merge taking up too much memory

Sorry for the very late answer. I've been looking for time to check the sources, but I just could

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merge taking up too much memory

Sorry for the very late answer. I've been looking for time to check the sources, but I just could

8/17/21

Katherine Chau, Jordi Camps2

8/17/21

sambamba syntax for mapped and unmapped reads

Hello, I think the main point is to know if you are interested in unmapped reads (as you said) or

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sambamba syntax for mapped and unmapped reads

Hello, I think the main point is to know if you are interested in unmapped reads (as you said) or

8/17/21

Phil Ewels

6/23/21

Understanding counts in markdup log

Hi there, I'm the developer for MultiQC and I'm currently reviewing a PR to add a module to

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Understanding counts in markdup log

Hi there, I'm the developer for MultiQC and I'm currently reviewing a PR to add a module to

6/23/21

Pjotr Prins

11/30/20

Sambamba v0.8.0 released!

https://github.com/biod/sambamba/releases/tag/v0.8.0 ## ChangeLog v0.8.0 (20201130) Maintainance

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Sambamba v0.8.0 released!

https://github.com/biod/sambamba/releases/tag/v0.8.0 ## ChangeLog v0.8.0 (20201130) Maintainance

11/30/20

Nalesh Jadhav

5/30/20

Getting a error while loading the vcf file

Dear Sir, I have been trying to load the VCF file by using the given protocol but there is a error

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Getting a error while loading the vcf file

Dear Sir, I have been trying to load the VCF file by using the given protocol but there is a error

5/30/20

Николай Роз, Pjotr Prins4

7/26/19

GSoC progress

CBAM introduction. Structure, performance and usage: https://gist.github.com/NickRoz1/

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GSoC progress

CBAM introduction. Structure, performance and usage: https://gist.github.com/NickRoz1/

7/26/19

Николай Роз

5/15/19

Nick Rozinsky GSoC Introduction

Hello Sambamba community! My name is Nick Rozinsky, and I am Pjotr Prins' GSoC student under Open

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Nick Rozinsky GSoC Introduction

Hello Sambamba community! My name is Nick Rozinsky, and I am Pjotr Prins' GSoC student under Open

5/15/19

Pjotr Prins

3/17/19

[sambamba-discussion] Sambamba v0.6.9 released!

See https://github.com/biod/sambamba/releases/tag/0.6.9

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[sambamba-discussion] Sambamba v0.6.9 released!

See https://github.com/biod/sambamba/releases/tag/0.6.9

3/17/19

Emilio, Pjotr Prins3

12/17/18

Sorting method for RSEM

Ok, thanks! Should it be a new comparator? I would need it with natural sorting, so I might have to

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Sorting method for RSEM

Ok, thanks! Should it be a new comparator? I would need it with natural sorting, so I might have to

12/17/18

Pjotr Prins

10/4/18

Sambamba v0.6.8 released!

An even faster sambamba with a number of fixes. See https://github.com/biod/sambamba/releases/tag/v0.

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Sambamba v0.6.8 released!

An even faster sambamba with a number of fixes. See https://github.com/biod/sambamba/releases/tag/v0.

10/4/18

Pjotr Prins

9/10/18

Sambamba pre-release v0.6.8

I just did a binary pre-release. It is faster than all previous versions and making it should be easy

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Sambamba pre-release v0.6.8

I just did a binary pre-release. It is faster than all previous versions and making it should be easy

9/10/18

amjad...@gmail.com

5/23/18

Sambamba sort question number of threads and memory

Hello I am using sambamba to sort bam files. I have 125 gb on my system. The t option allows

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Sambamba sort question number of threads and memory

Hello I am using sambamba to sort bam files. I have 125 gb on my system. The t option allows

5/23/18

Pjotr Prins, Emilio2

2/27/18

Sambamba vs samtools performance

Hi, the code of the tests I ran and a sample report can be found on GitHub at the following link:

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Sambamba vs samtools performance

Hi, the code of the tests I ran and a sample report can be found on GitHub at the following link:

2/27/18

AndrewW

2/20/18

Range violation or bug?

Hi everyone, I just tried this interesting sambamba tools and got an error as Range violation as

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Range violation or bug?

Hi everyone, I just tried this interesting sambamba tools and got an error as Range violation as

2/20/18

Emilio Palumbo, Pjotr Prins2

2/5/18

Cannot compile sambamba v0.6.7 on LInux

On Mon, Feb 05, 2018 at 02:56:43AM -0800, Emilio Palumbo wrote: > Hi, > I am trying to compile

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Cannot compile sambamba v0.6.7 on LInux

On Mon, Feb 05, 2018 at 02:56:43AM -0800, Emilio Palumbo wrote: > Hi, > I am trying to compile

2/5/18

br...@g.harvard.edu, Pjotr Prins2

1/3/18

Installation issues

Yes, sorry. The binary is for Linux only. I hope you can run Linux somewhere. On Mac you can do it in

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Installation issues

Yes, sorry. The binary is for Linux only. I hope you can run Linux somewhere. On Mac you can do it in

1/3/18

Joshua Randall, Pjotr Prins2

1/2/18

segmentation fault attempting to view header in json format

Hi Joshua, Thanks for reporting. I am getting the same error and created a github issue: https://

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segmentation fault attempting to view header in json format

Hi Joshua, Thanks for reporting. I am getting the same error and created a github issue: https://

1/2/18

Pjotr Prins

11/24/17

sambamba release 0.6.7

Minor release from the master branch https://github.com/biod/sambamba/releases * Adding ability to

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sambamba release 0.6.7

Minor release from the master branch https://github.com/biod/sambamba/releases * Adding ability to

11/24/17

Richard C, Pjotr Prins2

11/24/17

optical / proximal duplicates

Hi Richard, On Wed, Nov 22, 2017 at 08:39:13AM -0800, Richard C wrote: > Hi folks, > Once thing

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optical / proximal duplicates

Hi Richard, On Wed, Nov 22, 2017 at 08:39:13AM -0800, Richard C wrote: > Hi folks, > Once thing

11/24/17

Pjotr Prins, … Brad Chapman6

11/17/17

The future of sambamba - what to work on?

On Tue, Nov 14, 2017 at 07:05:49AM -0800, Brad Chapman wrote: > Great news that you have time and

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The future of sambamba - what to work on?

On Tue, Nov 14, 2017 at 07:05:49AM -0800, Brad Chapman wrote: > Great news that you have time and

11/17/17

Andrea Hobby, Pjotr Prins2

11/13/17

Question about installing binary file

Also looking at the output of https://gitlab.com/pjotrp/gnu-install-bin/issues/1, it looks like you

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Question about installing binary file

Also looking at the output of https://gitlab.com/pjotrp/gnu-install-bin/issues/1, it looks like you

11/13/17

Pjotr Prins

11/8/17

Pre-release of sambamba 0.6.7 available for download

You can install a binary of 0.6.7-pre1 for Linux from https://github.com/biod/sambamba#binary-

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Pre-release of sambamba 0.6.7 available for download

You can install a binary of 0.6.7-pre1 for Linux from https://github.com/biod/sambamba#binary-

11/8/17