Added support for calling CYP2D6 from targeted sequencing data
In general, accuracy for targeted datasets is less than that of WGS. This is largely due to difficulties with capture that lead to decreased coverage of hybrid or duplicated alleles.
We recommend using two additional parameters when using targeted sequencing data: --infer-connections --normalize-d6-only
Added two new CLI options to support targeted sequencing datasets:
--infer-connections - If set, pb-StarPhase will infer allele connections that are not observed in the dataset but common in the population. For example, 4 and 68 are commonly found together, as are 10 and 36. This option is recommended when reads are too short to directly span from one allele to the next.
--normalize-d6-only - If set, pb-StarPhase will only normalize the copy numbers using the CYP2D6 alleles (i.e., excluding any discovered CYP2D7 alleles). This option is recommended when coverage of the CYP2D7 alleles is inconsistent relative to the CYP2D6 alleles.
Fixed
Fixed a reporting issue in the PharmCAT TSV where brackets were missing from combination alleles
v0.10.0
Changes
--infer-connections --normalize-d6-only--infer-connections- If set, pb-StarPhase will infer allele connections that are not observed in the dataset but common in the population. For example, 4 and 68 are commonly found together, as are 10 and 36. This option is recommended when reads are too short to directly span from one allele to the next.--normalize-d6-only- If set, pb-StarPhase will only normalize the copy numbers using the CYP2D6 alleles (i.e., excluding any discovered CYP2D7 alleles). This option is recommended when coverage of the CYP2D7 alleles is inconsistent relative to the CYP2D6 alleles.Fixed