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Lifting over data #24

Closed ole-tange closed 11 years ago

ole-tange commented 11 years ago

This may or may not be handy when lifting over data:

http://www.pypedia.com/index.php/LiftOver_TPED_pipeline_user_Kantale http://genome.ucsc.edu/util.html

sapfo commented 11 years ago

Download the already existing one (mapped on hg19), Viictor will find a url

HapMap: ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/latest_phaseIII_ncbi_b36/plink_format/ HGDP: http://hagsc.org/hgdp/data/hgdp.zip (not sure what format this is though)

sapfo commented 11 years ago

Victor already looked at the Stanford version and everything is ok for strand and annotation but on build 36.

morenomayar commented 11 years ago

liftOver complete! I started from mike's version of HGDP, liftedOver the coordinates and checked rs# to be the same as dbSNP137 as provided in the GATK bundle. If the rs# was different, I kept the dbSNP one. There were 141 coordinates that could not be lifted. HGDP in mike format for hg 19 can be found in the GeoGen servers in /home/jmoreno/data/my_kelvin_data/MDSTests/HGDPdata/hg19