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Mitochondrial genome excluded from gatk workflow calling regions

Hi,
For the two files used to specify calling regions for GVCF and for joint calling:
gs://broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list
gs://gatk-test-data/intervals/hg38.even.handcurated.20k.intervals

... the mitochondrial contig is excluded. There is no reason why chrM should be excluded. Many people have clinically significant chrM variants. I think this is important to fix.

Thanks.

Answers

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