Preprocessing program for LumosVar

gvm is a tool that replaces the old LumosVar preprocess program.

Dependencies

Make sure the following are installed on your system:

• autotools (for building)
• htslib (>=1.4.1)
• libyaml
• gsl (>=2.4)
• gengetopt (for building)

The following dependencies are bundled as submodules:

• uthash

If you're on the dback cluster, running

$ source ./setup.sh

will load the modules that satisfy these dependencies. If not, you have to install them yourself.

Mac OS X

You can install the dependencies on OS X with homebrew.

$ brew install gengetopt gsl htslib libyaml

Cloning

Make sure to use --recursive when cloning.

$ git clone --recursive git@github.com:tgen/gvm

Building

Scripted

Run the following:

$ ./build.sh --init

And everything should get built. The gvm executable should be placed in the src directory. If dependencies were not met, the configure step will fail and tell you to install something. You can omit the --init on subsequent runs of build.sh

You can supply --debug to build a debug version and --clean to remove all generated files.

Manual

Run

$ autoreconf --install
$ ./configure
$ make

Running

Standard

Run

$ src/gvm --help

to see the options available. Generally you're going to want to do something like this:

$ src/gvm -c <path to your config.yaml> -C <chromosome to run on>

Normal Metrics

To calculate normal metrics, you have to set the flag for it (-N). However, you might also want to turn pos and exon file generation off and that is done with their respective flags as well (-P and -E). Note that all of these are toggles but -P and -E are on by default and -N is off.

If the YAML configuration is malformed for the task at hand, you might get a segmentation fault because I haven't had the chance to verify that I wrote the checks for every condition necessary to calculate normal metrics.

There is also a helper script that provides arguments with which -N must co-occur. The additional arguments are printed to standard output.

$ python scripts/nmconf.py conf.yaml 6
--ploidystr=222

So, a complete invocation of gvm for normal metrics calculation would be, given a conf.yaml that is made for normal metrics:

CONF=conf.yaml
CHR=6
NMOPTS=$(python scripts/nmconf.py $CONF $CHR)
gvm -c $CONF -C $CHR -P -E -N $NMOPTS

Note that there is nothing stopping you from running normal metrics as well as pos/exon file generation (supply -N but not -P nor -E) if you can provide the configuration that satisfies both tasks. This, however, has not been tested.