can vdjer work on whole-exome sequencing data?

[Coolgenome]

Hello,

can vdjer work on whole-exome sequencing data? or how to adjust the parameters to make it work for whole-exome sequencing data?

Thanks much!

[mozack]

Hi,

We've not tested on exome data. I would be skeptical about using exome data as the exome targets may not actually capture BCR sequences.

[Coolgenome]

Good morning and thank you so much for your prompt reply. We looked at our exome targets and quite sure that all the BCR gene segments were covered, that’s why we’d like to give it a try. In this case, what parameters do you suggest to change? Thanks much! From: Lisle Mose <notifications@github.com> Reply-To: mozack/vdjer <reply@reply.github.com> Date: Friday, August 11, 2017 at 7:59 AM To: mozack/vdjer <vdjer@noreply.github.com> Subject: Re: [mozack/vdjer] can vdjer work on whole-exome sequencing data? (#9) Hi, We've not tested on exome data. I would be skeptical about using exome data as the exome targets may not actually capture BCR sequences. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#9 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/Ade0B8G0deAIAM5s8D5pxi9_Kg3b3CJgks5sXFAvgaJpZM4O0F1I>. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

[mozack]

OK. Keep in mind that somatic hypermutation may have some impact on the capture.

I would suggest trying with the standard params and then try the sensitive mode if that yields no results.

[Coolgenome]

Many Thanks!
what's the default distance between V and J anchors? Do you suggest to change that?

[mozack]

For IGH we allow 10-90 nt between anchors and for IGK/IGL 0-60nt. I would expect those defaults to still be reasonable.