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Any experience about GQ settings #76

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AliceCheng7 opened this issue May 19, 2023 · 1 comment
Open

Any experience about GQ settings #76

AliceCheng7 opened this issue May 19, 2023 · 1 comment

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@AliceCheng7
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AliceCheng7 commented May 19, 2023

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
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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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