Pharmcat not interpreting phased vcf?

[Dafna-Mozand]

Hii,

I had a question about how and if pharmcat is analyzing phased data. I've got a vcf with phased data and it also shows as phased results in the report (screenshot).

It clearly shows that *28 and *80 are on the same allele so it should be *1/*28+*80 but it still says unphased data and that *28/*80 is also a possibility.

I was wondering what data I should provide to make sure it only gives the right possible diplotype according to the phased data.

vcf lines:
chr2 233759924 rs887829 C T 23.73 PASS F;PX=UGT1A1;AC=1;AN=2 GT:GQ:DP:AD:AF:PS 1|0:23:266:129,137:0.515:233759924
chr2 233760233 rs3064744 CAT CATAT,C,CATATAT 19.13 PASS F;PX=UGT1A1;AC=1,0,0;AN=2 GT:GQ:DP:AD:AF:PS 1|0:19:315:157,112:0.3556,.,.:233759924

If more information is needed please let me know.

Many thanks!
Dafna

[Dafna-Mozand]

Apparently it is because the reference calls have 0/0 and they should have 0|0 as well. I didn't realize that would make a big difference.

[markwoon]

Glad you figured it out.

If the main reason you're calling this out is because of the warning, that's something we can probably hide if the data is effectively phased.