Good Morning Stéphane: Here are the liftOver chain files for both directions (five lines in each):
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 ----- Original Message ----- From: "Stéphane Plaisance" <[email protected]> To: [email protected] Sent: Tuesday, April 24, 2012 9:33:51 AM Subject: [Genome] need rCRS liftover files for hs.MT I face a problem when trying to do population MT haplotyping from my NGS data. Rationale: The human MT sequence included in the h18 build (only one I checked so far) is not identical to the official MT reference used by the MITOMAP (rCRS = NC_012920.1) Consequently, when I use MT snp-lists obtained by human full genome re-sequencing, I cannot operate haplotyping using MITOMAP related tools (apples compared to pears). ClustalW results in Aligned Length = 16572 Gaps = 3 Identities = 16528 (99%) Request: Is there an easy way to create a liftover file (type used by UCSC) in order to lift my variant lists to the rCRS reference and compare my populations to existing population data. I found the UCSC liftover wiki pages but the 'chain and net' story is a bit hard to digest for me, I do not have blat running, and I am almost sure someone has already produced these liftover files. Sorry if I overloked something! Thanks a lot for your advice and help, Stephane _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
