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MuTect2 with BQSR flag

benjaminlmoorebenjaminlmoore Cambridge, UKMember

With HaplotypeCaller it's possible to perform BQSR on-the-fly rather than using PrintReads to write a recalibrated BAM beforehand. Now that MuTect2 runs on the GATK engine, is it possible to do the same thing? Maybe by passing multiple recal files (for normal and tumour)?

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Issue · Github
by Sheila

Issue Number
1101
State
closed
Last Updated
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Closed By
chandrans

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