GATK UnifiedGenotyper: calling "1/2" haplotypes
I've read this on a paper (the full paragraph can be found at the bottom):
"The UnifiedGenotyper of GATK allows for only one alternative, i.e. non-reference, allele to be called per site. "
I find it very strange, in fact I've look into my data and I can see "1/2" haplotypes. Is this a matter of older GATK versions?
They were using: v1.3-14-g348f2db
The full paragraph:
"The UnifiedGenotyper of GATK allows for only one alternative, i.e. non-reference, allele to be called per site. Thus, at positions of heterozygosity in which both alleles are non-reference alleles, only one allele can be described. To correct this issue and to reduce the potential reference bias that may be introduced by considering the reference sequence during genotype calling, positions where at least one non-reference allele was called for a certain individual were recalled as follows: (1) The reference genome was modified by replacing the reference allele with the alternative allele called in this individual. (2) GATK was run again using the modified reference genome with the same parameters as in the first iteration of genotype calling."