Migrating from P. falciparum reference genome 3D7 version 2 to version 3

Posted: 25 February 2013 by Alistair Miles in Uncategorized

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 test.v3.bed containing:

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
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"

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/

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