Help with converting files to BEAGLE format

BW22

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Join Date: Dec 2012

Posts: 2
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Help with converting files to BEAGLE format

12-08-2012, 08:13 PM

Hello,
I am a clinical geneticist (MD) with little bioinformatics background, but I am trying to teach myself how to analyze my research exome data by myself... I don't want to miss out on the fun!
I have been able to convert my .vcf files to ped/map files (plink format).
I am now trying to convert either my vcf file to Beagle format or my ped/map files to Beagle format files.
I am encountering all sorts of problems.
I've tried using a germline utility with Beagle, but to no avail.
I was wondering if someone could give me simple- step-by-step instructions on how to do this.
I would really appreciate it!
Thanks.
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NBlackburn

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Join Date: Mar 2012

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#2

12-09-2012, 07:45 PM

Hi BW22,

It's certainly not a step by step answer but I stumbled across this whilst looking for something else and remembered your question:

Page Redirection

http://vcftools.sourceforge.net/options.html#other_format

Requires you to install vcftools of course, but maybe someone else can give step by step instructions.

Nicholas Blackburn | PhD Candidate
Tasmanian Inherited Cancer Centre
Menzies Research Institute Tasmania
Hobart TAS 7000 | www.menzies.utas.edu.au
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