Question

Vaast Script (Perl / Shell)

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12.5 years ago

Mpiro • 0

I am trying to use VAAST (www.yandell-lab.org) for Variant Annotation, and Analysis.

I was wondering if anyone knows any Shell / Perl script or practical that I can use to incorporate it in my pipeline.

Appreciate your comments.

Thanks,

script pipeline annotation • 1.9k views

ADD COMMENT • link updated 12.5 years ago by Zev.Kronenberg 12k • written 12.5 years ago by Mpiro • 0

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Your question is unclear. Are you looking for existing scripts to use in a pipeline, or a resource for learning sh/perl scripting in general?

ADD REPLY • link 12.5 years ago by Neilfws 49k

score 1 · Answer 1 · 2011-11-07

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12.5 years ago

Zev.Kronenberg 12k

Currently I don't believe our lab has any scripts that will do this. What are you trying to accomplish?

-Zev Yandell Lab

ADD COMMENT • link 12.5 years ago by Zev.Kronenberg 12k

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VCFformat->GVFformat->VAT->VST->VAAST.

as for as making this process faster i like to create a giant CDR file and use ~/tools/vaast2/bin/vaasttools/cdrmanipulator.pl to pull out individuals.

ADD REPLY • link 12.5 years ago by Zev.Kronenberg 12k