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caleblareau / mgatk

mgatk: mitochondrial genome analysis toolkit
http://caleblareau.github.io/mgatk
MIT License
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cambridge mitochondrial genome #3

Closed caleblareau closed 6 years ago

caleblareau commented 6 years ago

@julirsch vaguely remember you talking about this

https://www.mitomap.org/foswiki/bin/view/MITOMAP/HumanMitoSeq

What is there to do here / how important is this?

julirsch commented 6 years ago

My understanding is that this is an "improved" sequence of the European mitochondrial genome. Using this instead of the standard distribution hg19 fasta would probably get rid of some fake "polymorphisms" that are present in all cells. Probably would want to implement this at the alignment stage (probably slightly better alignments too) so maybe worth doing once we account for mtDNA circularity but not until?

caleblareau commented 6 years ago

RCR is in GRCh37 + or hg38