Description

PennCNV, a hidden Markov model (HMM) based approach, is for kilobase-resolution detection of copy number variations (CNVs) from Illumina high-density SNP genotyping data. This algorithm incorporates multiple sources of information, including total signal intensity and allelic intensity ratio at each SNP marker, the distance between neighboring SNPs, the allele frequency of SNPs and the pedigree information where available.

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 penncnv
-------------------- /usr/local/Modules/3.2.9/modulefiles ----------------------
penncnv/current(default)

$ module load penncnv

$ module list
Currently Loaded Modulefiles:
  1) penncnv/current

$ module unload penncnv

$ module load penncnv/current

$ module show penncnv
-------------------------------------------------------------------
/usr/local/Modules/3.2.9/modulefiles/penncnv/current:

module-whatis    Sets up penncnv 
prepend-path     PATH /usr/local/apps/penncnv/current 
-----------------------------------------------------------------

How to Use

PennCNV can be run on helix or biowulf cluster. If your job is going to take a long time or require tons of memory, we recommend running it on biowulf node. User can apply for a biowulf account at http://biowulf.nih.gov/user_guide.html#account.

Example

The sample run below is based on the instruction on http://www.openbioinformatics.org/penncnv/penncnv_examples.html . The sample input files can be copied from /usr/local/apps/penncnv/current/example on helix or biowulf. The sample run is taking place on helix but can also run on a biowulf node (do not run on biowulf login node). See instructions on http://biowulf.nih.gov/apps/penncnv.html

Copy sample files to your current working directory:

$ module load penncnv
$ cd /data/$USER/Dir1
$ cp -r /usr/local/apps/penncnv/current/example .
$ cd example
% ./runex.pl --path_detect_cnv detect_cnv.pl 1
% ./runex.pl --path_detect_cnv detect_cnv.pl 2
% ./runex.pl --path_detect_cnv detect_cnv.pl 3
% ./runex.pl --path_detect_cnv detect_cnv.pl 4
% ./runex.pl --path_detect_cnv detect_cnv.pl 5
% ./runex.pl --path_detect_cnv detect_cnv.pl 6
% ./runex.pl --path_visualize_cnv visualize_cnv.pl 7
% ./runex.pl --path_convert_cnv convert_cnv.pl 8
% ./runex.pl --path_convert_cnv convert_cnv.pl 9
% ./runex.pl --path_filter_cnv filter_cnv.pl 10
% ./runex.pl --path_compare_cnv compare_cnv.pl 11
% ./runex.pl --path_compare_cnv compare_cnv.pl 12
% ./runex.pl --path_infer_allele infer_snp_allele.pl 13
% ./runex.pl --path_infer_allele infer_snp_allele.pl 14

Documentation

http://www.openbioinformatics.org/penncnv/penncnv_examples.html