How to get the GL for multi variants (multi-allelic)

[cxue]

According to for format of GL(GL # Genotype log-likelihoods (natural log) for AA,AB and BB genotypes, where A = ref and B = variant. Only applicable for bi-allelic sites). How to get GL for multi-allelic variants? I can not understand, Platypus can output GT for multi-allelic without GL.

[andyrimmer]

Hi,

Platypus does not currently output genotype likelihoods for multi-allelic
sites. There is no option to do this yet. Several people have asked for
this, and I would
like to implement it, but do not have the time right now.

Kind regards,
Andy

On Wed, Oct 8, 2014 at 5:46 PM, cxue notifications@github.com wrote:

According to for format of GL(GL # Genotype log-likelihoods (natural log)
for AA,AB and BB genotypes, where A = ref and B = variant. Only applicable
for bi-allelic sites). How to get GL for multi-allelic variants? I can not
understand, Platypus can output GT for multi-allelic without GL.

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