I’ve created a liftover chain file to migrate genomic data from the “version 2” 3D7 reference genome to the newer “version 3” reference genome. You can download the chain file at the link below, as well as a binary for the liftOver program compiled for x86_64:
To check it works, download the above and test.bed to a local directory then run:
chmod +x ./liftOver ./liftOver test.bed 2to3.liftOver test.v3.bed test.v3.unmapped
This should create the file
Pf3D7_07_v3 403620 403621 crt
Note that this expects chromosome names in the input to be like “Pf3D7_01”. If you’re using chromosome names like “MAL1” you’ll need to convert those first prior to applying the liftover to version 3.
To build the
liftOver binary (and the other programs that are needed to create the liftover file) I did the following on Ubuntu 12.10:
wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip unzip jksrc.zip -d jksrc cd export MACHTYPE=x86_64 mkdir ~/bin/$MACHTYPE export PATH=~/bin/$MACHTYPE:$PATH sudo apt-get install libmysqlclient-dev export MYSQLINC=/usr/include/mysql export MYSQLLIBS="/usr/lib/x86_64-linux-gnu/libmysqlclient.so.18 -lz" make
This didn’t completely build, but it got far enough to build the binaries in ~/bin/x86_64/ needed to create the liftover chain file.
To create the liftover chain file I followed instructions found at these links:
This liftover was built using the following versions of the 3D7 reference genome:
- “version 2”: ftp://ftp.sanger.ac.uk/pub/pathogens/Plasmodium/falciparum/3D7/3D7.latest_version/September_2011/
- “version 3”: ftp://ftp.sanger.ac.uk/pub/pathogens/Plasmodium/falciparum/3D7/3D7.latest_version/version3/September_2012/