Enable output of mitochondrial variants

[phillip-richmond-alamya]

Is your feature related to a problem?

There are no mitochondrial variants reported in the output SNP file

Describe the solution you'd like

It looks like the haplotagged.bam doesn't output reads over chrM, but the pre-haplotagging BAM does.

Describe alternatives you've considered

I'm using this pipeline, it should output these well covered genomic variants.

Additional context

I think clair3 should still call them?

[RenzoTale88]

@phillip-richmond-alamya the default behaviour of the workflow is to consider only the chromosomal sequences. You can override this behaviour by setting --include_all_ctgs at run time, and you should also generate the variants for chrM.

[phillip-richmond-alamya]

Ahhhh thank you!! Simple fix!