Annotation update for chrM

[jemten]

Description

The mitochondria can be encoded as either MT or chrM in the vcf. In the annotation step, genmod has a special rule for the mitochondria but it only kicked in when the mitochondria was encoded as MT. This PR changes the internal representation of the mitochondrial chromosome to 'M'.

Fixed

• genmod annotate for mitochondrial variants when using the chrM notation

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_[TOOL]-t [TOOL] -b [THIS-BRANCH-NAME] -a

How to test

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Expected test outcome

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• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
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This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

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• Deploy this branch on ...
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