lifting over mitochondrial SNPs between reference genomes

Question

[112233]

Hi!I have mtDNA SNPs in a VCF file. I am fairy certain they were found by hg19 as a reference. I think they used a patched version (GRCh37p13 maybe??), but I'm not totally sure how to check that. I concluded that they used this version of the reference genome (chrMT, not chrM) just by briefly comparing the sequences I found here: https://genome.ucsc.edu/cgi-bin/hgc?hgsid=2718626402_mXM6sT6UAuZKAaa9F279og3JpwHP&g=htcCdnaAli&i=chrM&c=chrMT&l=0&r=16569&o=0&aliTable=altSeqLiftOverPsl.

Do I need to do a liftover to GRCh38/rCRS? Or is it good as is? If I do need to lift over to the newer edition, are there specific tools that are good for mtDNA SNPs

Answer 1

[benformatics]

hg19 and hg38 are generally focused on the autosomes.

IIRC hg19 assemblies can be mixed with some using the rCRS (16569 bp) and some using a Yoruban reference (16571 bp).

The standard is now to use the rCRS one NC_012920.1

To lift over you need to figure out which matches your reference. I would recommend spot checking the variants to see if the REF matches or not.

I think there is a spacer somewhere in the new version to keep variants homogenized.

Check out mitomap.org they have more info

[Jeremy Leipzig]

the chrM length is probably in the VCF header