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Outside Call Format

Typically, PharmCAT uses variant call data to match diplotypes used to find annotations. However, you can also give diplotypes to PharmCAT that were called by other tools. This is especially useful for genes that PharmCAT will not match like CYP2D6.

These outside call files can be supplied to the overall PharmCAT tool using the -a flag or to the Phenotyper using the -o flag.

File format

The outside call file format is a tab-separated file.

Each line starts with the HGNC gene symbol, then a tab, then the diplotype (e.g. *1/*3). Lines starting with # will be ignored.

Here’s an example of an outside call file:

CYP2D6	*1/*3
G6PD	B (wildtype)/B (wildtype)
MT-RNR1	1555A>G

PharmCAT is managed at Stanford University & University of Pennsylvania (NHGRI U24HG010862)