I am currently trying to have star alleles called on my phased vcf file. So far I have a vcf file with a few thousand samples that has been phased with BEAGLE 5.2.
The next step is to run PGx-POP to obtain star allele calls, however when I run it, I mainly have only *1's called in the haplotype 1 and haplotype 2 any phenotypes with either "Not available" or "Normal function".
This is what I used to run the script:
python 3.6 PGxPOP.py --vcf MyPhasedVCF --phased -o PGxPOP_output.txt
I even looked up a table of SNPs associated with star alleles and ran a manual grep for a SNP (rs1057910) associated with a *2 allele with gene CYP2C9 to make sure it was in my dataset and the genotype definitely showed up in more than one sample.
Any idea what I could be doing wrong? Is my vcf phased incorrectly? Any troubleshooting ideas I could try?
Thank you kindly!