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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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interpreting d67_snp_* fields in json output #13

Closed mgonzalezporta closed 2 years ago

mgonzalezporta commented 2 years ago

Hi Xiao,

We're trying to reproduce these 2 figures from the Cyrius manuscript:

image

We've identified the relevant fields from the json output to be used, namely d67_snp_call and d67_snp_raw for panel B, and Variants_called for panel C.

Since the d67_snp_* fields are not annotated with variant information, we wanted to confirm that we're interpreting them correctly. Are we OK to assume that each differentiated variant appears in the same order as in the bundled annotation files (https://github.com/Illumina/Cyrius/blob/master/data/CYP2D6_SNP_38.txt)?

Thanks in advance!

xiao-chen-xc commented 2 years ago

Hi @mgonzalezporta

Yes that is correct. The order is the same as in the CYP2D6SNP*.txt resource file.

Thanks, Xiao

mgonzalezporta commented 2 years ago

Thanks!