call

define INFO:tier based on code in report
add CRAM support

normalise

migrate to pyvcf where possible
Should document how we combine variants

merge

migrate to pyvcf where possible (started in dev/merge2.py)
force the same sample names in the same order in mity and HC?
are there any VCF format 4.1 vs 4.2 fields that clash. eg the type of the variable changes?

report

mity report fails if mity normalise hasn't been run, so consider making this mandatory & dropping mity normalise
Check if report works with multiple VCFs
update mitomap annotations

misc

use logging.info, logging.debug, logging.warning, logging.error where possible
hg19 support: after running BLAST, there are more sequence differences than initially appreciated. This is scheduled for deprecation

DNAnexus

migrate app code to use the latest mity. either via an asset, or Docker image.