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
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Stephane Plaisance
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
Hi, nice you got the answer and posted the conversation here, do you maybe want to merge your accounts? I assume you are the same person Stephane?
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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.