TABIX

Sep 18, 2012 at 10:14 PM

Hi there,

tabix is a part of samtools for Linux, do you have its equivalent for Windows?

A

Coordinator
Sep 19, 2012 at 9:57 AM

Hi,

It seems that tabix isn't in the 1000 genome project pipeline or any other project i'm aware of. I just had a look of the source on github, the code base is very old, and full of comments like 'buggy', 'error' etc. So I wonder maybe people already moved on to something new?

I could of cause port this to Windows, if there is no other solution around. Do you mind give some examples of the use case here?

Best,

dong

Sep 25, 2012 at 5:14 PM
Hi Dong,
Thank you for your email and sorry for the delayed response. I am using tabix when i have a large tab delimited list of genomic coordinates that i want to search for in my VCF file. Someone on the forum had suggested that tabix was the way to do it and it seems like it works. I believe many people create rich annotation of vcf files which i why you may not much usage of tabix.

If you can port this to windows that would be great, actually it would be awesome if you code has .NET managed API. i.e. at least have .NET wrappers instead of having to call them from command line.

Let me know what you decide.

Ashwin


From: [email removed]
To: [email removed]
Date: Wed, 19 Sep 2012 02:57:23 -0700
Subject: Re: TABIX [bow:396001]

From: xied75
Hi,
It seems that tabix isn't in the 1000 genome project pipeline or any other project i'm aware of. I just had a look of the source on github, the code base is very old, and full of comments like 'buggy', 'error' etc. So I wonder maybe people already moved on to something new?
I could of cause port this to Windows, if there is no other solution around. Do you mind give some examples of the use case here?
Best,
dong
Read the full discussion online.
To add a post to this discussion, reply to this email (bow@discussions.codeplex.com)
To start a new discussion for this project, email bow@discussions.codeplex.com
You are receiving this email because you subscribed to this discussion on CodePlex. You can unsubscribe on CodePlex.com.
Please note: Images and attachments will be removed from emails. Any posts to this discussion will also be available online at CodePlex.com
Coordinator
Oct 3, 2012 at 10:05 AM

Hi, Ashwin,

I had a quick look of the source code, many files are used in BWA and SAMTOOLS, so shouldn't be a problem to port. I'll see if I can finish something asap.

Best,

dong

Oct 3, 2012 at 4:51 PM
Thanks, this is great. I think it will be a really good addition to the porting that you have already done.

Ashwin


From: [email removed]
To: [email removed]
Date: Wed, 3 Oct 2012 03:05:31 -0700
Subject: Re: TABIX [bow:396001]

From: xied75
Hi, Ashwin,
I had a quick look of the source code, many files are used in BWA and SAMTOOLS, so shouldn't be a problem to port. I'll see if I can finish something asap.
Best,
dong
Read the full discussion online.
To add a post to this discussion, reply to this email (bow@discussions.codeplex.com)
To start a new discussion for this project, email bow@discussions.codeplex.com
You are receiving this email because you subscribed to this discussion on CodePlex. You can unsubscribe on CodePlex.com.
Please note: Images and attachments will be removed from emails. Any posts to this discussion will also be available online at CodePlex.com