Does anyone know of a command line tool taking a list of MT-chromosome SNVs (mapped against hg18, not against the original NCBI chromosome MT!) and able to return the most likely MT haplogroup for that genome? thanks! Stephane
Here is the long awaited answer freshly contributed by Hiram Clawson from genome@soe.ucsc.edu
Thanks Hiram
REM: to use these liftover chains, copy them to a map.chain file and apply the ucsc tool command like: 'liftOver hg18/19.bed-file map.chain rCRS.bed-file unMapped'
Liftover chain from chrM_rCRS to UCSC hg18/hg19 chrM:
chain 1550477 chrM_rCRS 16569 + 0 16569 chrM 16571 + 0 16571 230
310 0 2
2796 1 0
13075 0 1
387
Liftover chain from UCSC hg18/hg19 chrM to chrM_rCRS:
chain 1550477 chrM 16571 + 0 16571 chrM_rCRS 16569 + 0 16569 230
310 2 0
2796 0 1
13075 1 0
387
-Hiram
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This leaves me a bit confused, maybe because I misunderstood something... The mitochondrial chromosome is inherited for the mother only as a whole (+random mutations, afaik). Does it make sense to talk of a haplotype for a MTchr? Would the definition of haplotype not require the presence of recombinant events, and do such event affect MT? Or put differently wouldn't each MTchr be a complete haplo-block by itself?
Hi Michael! I took the naming from the web pages where I read about it. This is the terminology used everywhere and it reads 'haplogroup' and not 'haplotype'. Thanks for your post, I hope someone else has a solution to my problem which has to do with a difference between the Cambridge Reference Sequence (rCRS; NC_012920.1) used for haplogroups and the hg18 build36 used to call my MT variants. A liftover method to convert my calls to rCRS is what I need.
Thanks for the clarification, I just didn't know enough about it it seems. Seemingly this question was too tough for BioStar. It looks like we are currently not so strong in the field of genetics.