About track of HapMap LD Phased, thanks!

[xiaoming-Zhong]

Hi, dear UCSC members!

I have a vcf file and phase it with SHAPEIT, and I try to calculated LD, r-squre, and LOD with HaploView now. There is a track  named "HapMap LD Phased" in hg18 that display these parameters, but I can't find a way to do the same thing. After google, I found some one had asked whether he could load track as custom track but it was impossible. Since I had mirror the browser, can I supply a track as hg18. If I can, how should I do after I finished the step of HaploView?

Thanks!

Best wishes!

                                                                                                                                        Xiaoming Zhong

[Steve Heitner]

Hello, Xiaoming.

If you would like to recreate this track, you can view the original SQL definitions and the procedure used to create the original track.  Since the HapMap LD Phased track is a composite track containing three subtracks, there are three hapmapLdPh*.sql files located at http://hgdownload.soe.ucsc.edu/goldenpath/hg18/database/.  The procedure used to generate the original track is contained in the hg18 make doc in our source tree at http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/hg/makeDb/doc/hg18.txt.  Look for the section titled “HAPMAP LD”.

Please contact us again at genome...@soe.ucsc.edu if you have any further questions.  Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users.  If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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