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.
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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