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5.4 years ago
bioinfo89
▴
50
Hello All,
I have few variants from chr M for which I want to convert the coordinates for these variants from previous version NC_001807.4 to the latest version NC_012920.1. Is there any way to do this?
I tried using the liftover tools but I am unable to select any assembly version which is mentioned for chrM.
Any suggestions will be appreciated.
Thank you!
Hi bioinfo89
That's appears to be difficult because RefSeq NC_001807 is an African (Yoruban) sequence with over 40 variant nucleotides from the rCRS. On July 8, 2009 the sequence was removed from GenBank as a reference sequence but may be found. The rCRS has a new number in GenBank! It is now officially NC_012920.1. Unfortunately, mistaken use of this Yoruban sequence as the rCRS is still seen occasionally in new publications today.
Source: https://www.mitomap.org/MITOMAP/HumanMitoSeq
A related biostar post is here
Yes that's true but the hg19 reference (UCSC version) uses NC_001807 version for chrM mentioned here : http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/.
It has not been updated to the NC_012920.1 for hg19. This is the reason why I want to convert my variants to the latest version but I am not sure how to do this.