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Issue with GenotypeGVCFs - GATK 4.0.10.1

KousikKousik GermanyMember

Hi,
I have got a problem running GenotypeGVCFs. The error is mentioned below.

A USER ERROR has occurred: Bad input: malformed RAW_MQ annotation: 2346838272,3678071

Apparently, it seems the issue has been raised on GitHub but has not been addressed yet. Here is the link:

https://github.com/broadinstitute/gatk/issues/5433

I was wondering whether anyone could give me a quick solution for it. Thank you.

Cheers,
Kouisk

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