optiCall on Helix
optiCall is designed to make accurate genotype calls across the minor allele frequency spectrum. Using intensity information from across multiple individuals and multiple SNPs when calling genotypes, allows it to call both rare and common variants accurately.
When citing optiCall please use this paper.
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
$ module avail opticall -------------------- /usr/local/Modules/3.2.9/modulefiles ---------------------- opticall/0.6.4(default) $ module load opticall $ module list Currently Loaded Modulefiles: 1) opticall/0.6.4 $ module unload opticall $ module load opticall/0.6.4 $ module show opticall ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/opticall/0.6.4: module-whatis Sets up optiCall 0.6.4 prepend-path PATH /usr/local/apps/opticall/0.6.4 -----------------------------------------------------------------
Sample session on Helix
Sample file can be copied from /usr/local/apps/opticall/0.6.4/example.int and example.info:
$ mkdir /home/$USER/dir1;cd /home/$USER/dir1 $ cp /usr/local/apps/opticall/0.6.4/example.* .
The run:
$ module load opticall $ opticall -in example.int -out example.out
Documentation
