Hi! I have received a GWAS dataset to analyze mitochondrial haplogroups that I pretend to do with HaploGrep2. As I understand HaploGrep2 uses rcrs as reference. My data have been mapped against human genome build 37, but the Illumina technical support told me that both, build 37 and build 38 of the human genome include rcrs. As I found some different opinions in the internet I was wondering if there exist any way to confirm which version of the mitochondrial genome was used to map my dataset. Has anybody have some advice on how to confirm that? I have already analyzed my data with HaploGrep2, and the results make sense, despite that they have a poor quality. Anyway, I would like to make shure that I am analyzing correctly. Any advice would be great!!!!
i'm confused as to how you obtained your sequences (microarray->injection vs actual sequencing), but if it they weren't mapped rCRS positions your results would likely be full of really weird variants, especially after position 3107. build37 has rCRS unless you use the UCSC hg19 version