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Hello! I was wondering if the HaplotypeScore annotation was restored for HaplotypeCaller in GATK 2.6. Does it have to be called? (It's not included in my vcf file.) Moreover, all of the GT field designations have "/" instead of "|" which according to the following would mean that the results are still unphased:
"GT genotype, encoded as alleles values separated by either of ”/” or “|”, e.g. The allele values are 0 for the reference allele (what is in the reference sequence), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1 or 1|0 etc. For haploid calls, e.g. on Y, male X, mitochondrion, only one allele value should be given. All samples must have GT call information; if a call cannot be made for a sample at a given locus, ”.” must be specified for each missing allele in the GT field (for example ./. for a diploid). The meanings of the separators are:
/ : genotype unphased
| : genotype phased"
http://www.1000genomes.org/wiki/Analysis/Variant Call Format/vcf-variant-call-format-version-40
Also, is there a more detailed explanation than what's on the HaplotypeScore documentation page? How is the score determined in UnifiedGenotyper? Does the score have anything to do with phasing? Also, how is phasing achieved if only the 10bps surrounding the SNP are examined, regions which likely do not include other SNPs?