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Old 06-13-2012, 09:18 AM   #1
Location: USA

Join Date: Mar 2012
Posts: 21
Default Help using Shapeit

I'm trying to infer haplotypes from a trio dataset using shapeit.

I have 3 VCF files for variants which I converted to plink/map PED formats with VCF tools.

I have further split the data by chromosome using pLink and I'm trying to tun shapeit on these files.

The software seemed to work well for the example dataset provided but it seems to crash for my dataset at the pruning stage without reporting any errors.

if anyone has any experience dealing with a similar project I'd like to learn about their experience.
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Old 03-26-2014, 05:41 PM   #2
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Location: China

Join Date: Feb 2012
Posts: 1

I meet the same problem with you, have you solved it now? Can you share me your experience?
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Old 03-26-2014, 07:13 PM   #3
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Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190

I recently used something called AlphaPhase that worked pretty fast, the downside was that it can only take bi-allelic SNPs.
Jeremy is offline   Reply With Quote

halpotype, phasing, shapeit, trio

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