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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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Cyrius v1.1.1 incorrectly calls GeT-RM sample NA18565 that was correctly called by Cyrius v1.1 #33

Open VasilisFlouris opened 1 year ago

VasilisFlouris commented 1 year ago

Hello there,

while testing Cyrius v1.1.1 on CYP2D6-calling on samples from GeT-RM I encountered something unexpected. On a publication that used Cyrius v1.1, sample NA18565 is correctly genotyped as 10/36x2 (supplementary materials). Nevertheless, v1.1.1 that I used calls this sample as 36/36+*10.

The BAM file for this sample was downloaded from the ENA website and used as is.

Cyrius was called as:

python3 star_caller.py --manifest manifest.txt --genome 37 --prefix prefix --outDir outdir

Could this be due to an error on my end?

Thank you.

xiao-chen-xc commented 1 year ago

Hi @VasilisFlouris

36/36+10 is indeed what Cyrius would call this sample. All three star alleles are matching with 10/36x2. The difference is in how the haplotypes are assigned into two alleles. Based on short read data, it is not clear whether the two copies of 36 are on the same allele, and Cyrius outputs what it thinks is more likely. I'm not sure whether the exact phasing of 10/36x2 has been confirmed by any technology.

Thanks, Xiao