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Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF
Apache License 2.0
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Any experience about GQ settings #76

Open AliceCheng7 opened 1 year ago

AliceCheng7 commented 1 year ago

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 commented 1 year ago

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).