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Any experience about GQ settings #76

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AliceCheng7 opened this issue May 19, 2023 · 1 comment

AliceCheng7 commented May 19, 2023 •

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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

Collaborator

jzieve commented May 19, 2023

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).

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