Any experience about GQ settings

[AliceCheng7]

Hi team,
Could you help to explain the meaning of GQ? what is the GQ range? Can we try to use the GQ to filter low-confidence calls?
Best,
Xianying

[jzieve]

This white paper explains the gencall score: https://www.illumina.com/Documents/products/technotes/technote_infinium_genotyping_data_analysis.pdf which is what GQ reflects, but phred-scaled in this tool.
It can be filtered for low-confidence calls as you see fit.

I would recommend using the tool linked here however: https://github.com/Illumina/GTCtoVCF#semi-archived-state as that reports the raw GQ/Gencall (not phred-scaled).