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

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:


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


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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