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GQ and PL fields #236

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mashid opened this issue Jan 9, 2024 · 0 comments

mashid commented Jan 9, 2024

Hello.

For GATK GQ value is equal to the second smallest PL (https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format). But this is wrong for our result. Could you explain how GQ and PL are calculated and related?

Example of our result:

Best regards, Maria

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