Why is GATK4.3 give inconsistent outputs?

23 February 2023 0 7K Report

When I run ApplyBQSR two of my samples generate all the chromosome lists and then MT. For the other samples that came from a similar pipeline, MT is not available in the list. Surprisingly, the sample was taken from the same breed, processed with a similar upstream pipeline, and checked for availability of MT in dedup.bam before running ApplyBQSR.

Thank you in advance for your valuable suggestions!

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