Question about the genotype format (GT) in the output file #8

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marcelo-ra opened this Issue Mar 16, 2011 · 1 comment

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For a pooled sample where there are reads of 2 diploid organisms (--ploidy=4) let's pretend that the genotype output (GT) of freebayes is:

1/1/1/0

As I understand it, the first two ones (1/1..) represent the genotype of the first organism while the rest of the numbers (..0/1) represent the genotype of the second organism. Is this interpretation correct?

Thanks in advance

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ekg commented May 17, 2011

The pooled genotypes are not phased, so no indication is made about the genotype of the first or second organism. The call of 1/1/1/0 simply means that there are three ALT alleles and one REF allele in the pool.

@ekg ekg closed this Oct 2, 2013

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