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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Version 0.2.5a8 #14

Closed boboppie closed 9 years ago

boboppie commented 9 years ago

Dear @liangkaiye ,

Version 0.2.5a8 has been used in intansv (http://andrewhzau.github.io/intansv/) and metasv (http://bioinform.github.io/metasv/), however I can't find in it the repository, can you help?

Best wishes, Fengyuan

liangkaiye commented 9 years ago

The Pindel official repository is at https://github.com/genome/pindel

On 5/12/15 9:12 AM, Fengyuan Hu wrote:

Dear @liangkaiye https://github.com/liangkaiye ,

Version 0.2.5a8 has been used in intansv (http://andrewhzau.github.io/intansv/) and metasv (http://bioinform.github.io/metasv/), however I can't find in it the repository, can you help?

Best wishes, Fengyuan

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/issues/14.

boboppie commented 9 years ago

Hi @liangkaiye ,

Thanks. But 0.2.5a8 is not on the release page - https://github.com/genome/pindel/releases

Best wishes, Fengyuan

EWLameijer commented 9 years ago

Hi Fengyuan,

My name is Eric-Wubbo Lameijer, I usually focus on the Pindel2vcf. However, I hope that you and Kai don't mind me intervening in this discussion.

As far as I can gather, version 0.2.5.a8 is the release at (or any release after) October 14, 2014. See

https://github.com/genome/pindel/commits/master

at the header

Commits on Oct 14, 2014

    remove one bug in GetRealStart4Deletion, updated version number

    liangkaiye
   authored on Oct 14, 2014

Unfortunately, as the version number has not been updated since, the 0.2.5.a8 version used could in theory be any of the 4 updates since. However, since most updates just modified pindel2vcf or are very recent/experimental/not fully implemented yet, I think that that October 14, 2014 commit would be the one you are looking for, at

https://github.com/genome/pindel/tree/453782df16c63f8aaff2d383a49b3fffda24110c

I hope this helps!

Best wishes,

Eric-Wubbo

Date: Tue, 12 May 2015 08:08:36 -0700 From: notifications@github.com To: pindel@noreply.github.com Subject: Re: [pindel] Version 0.2.5a8 (#14)

Hi @liangkaiye ,

Thanks. But 0.2.5a8 is not on the release page - https://github.com/genome/pindel/releases

Best wishes,

Fengyuan

— Reply to this email directly or view it on GitHub.

boboppie commented 9 years ago

Dear Eric-Wubbo,

Thank you very much for the information! I'll check out that commit.

Best wishes, Fengyuan