Question: (Closed) How to calculate genotype (GT) likelihoods ?
0
gravatar for pinninti1991reddy
10 months ago by
pinninti1991reddy30 wrote:

Hi I very confused, regarding biallelic and multiallelic genotype (GT) likelihoods, how it is calculated ?

F(j/k) = (k*(k+1)/2)+j.

can any one explain. Thanks

sequencing snp genome • 562 views
ADD COMMENTlink modified 9 months ago by RamRS19k • written 10 months ago by pinninti1991reddy30
1

where did you find this equation ?

ADD REPLYlink written 9 months ago by Pierre Lindenbaum115k

Sorry, for late response. Can you go through this link https://github.com/samtools/hts-specs/blob/master/VCFv4.2.pdf page no.6 Genotype likelihoods

ADD REPLYlink written 9 months ago by pinninti1991reddy30
1

That's for GL, not GT.

ADD REPLYlink written 9 months ago by RamRS19k

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time. Formatting bar

ADD REPLYlink written 9 months ago by RamRS19k

Hello pinninti1991reddy!

Please follow up on your questions. See C: Readgroups for a bam file ?

For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 7 months ago • written 7 months ago by RamRS19k
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