TRHarmonizer Library Details¶
Here are details about how the harmonizer library (and the TRTools which are built on top of it) handle VCFs produced by the different supported genotypers.
Different callers will call alleles differently (sequences or just lengths, if sequences with or without impurities such as partial repeats or internal SNPs, if sequences with or without flanking SNPs)
AdVNTR - Calls sequence genotypes with impurities.
ExpansionHunter - Calls lengths genotypes.
GangSTR - Calls sequence genotypes without impurities.
HipSTR - Calls sequence genotypes with impurities. Can call flanking base pairs and SNPs, if so TRRecord will have
trtools.utils.tr_harmonizer.TRRecord.GetFullStringGenotypes(). HipSTR does not report the underlying motif, so it is inferred from the sequence, which is usually but not always correct.
PopSTR - Calls the reference as a sequence genotype with impurities. Calls alt alleles as length genotypes.
Quality scores are numbers associated with each call in a VCF where a higher number means a better call. The reliability of these numbers is dependent on the genotyper that emitted them. Here is how TRHarmonizer infers quality scores for each supported genotyper:
AdVNTR quality scores are taken directly from the
ML(maximum likelihood) format field.
ExpansionHunter does not output a quality score. It does output a confidence interval, but this field is not currently used by TRTools.
GangSTR quality scores are taken directly from the
HipSTR quality scores are taken directly from the
Qformat field. TRHarmonizer ignores the
PQfield, which represents the quality of a call and its phasing.
PopSTR does not output a genotype quality score. It does output a
PLfield with Phred-scaled genotype likelihoods, but this field is not currently used by TRTools.
More details about these fields can be found in the documentation for each genotyper.