Biowulf High Performance Computing at the NIH
PennCNV: Copy Number Variation (CNV) detection from SNP genotyping arrays

PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn0862 ~]$ module load penncnv
[+] Loading penncnv  1.0.5    
[user@cn0862 ~]$  -h
Usage: [arguments] 

     Optional arguments:
            -v, --verbose                   use verbose output
            -h, --help                      print help message
            -m, --man                       print complete documentation

            Analysis Type:
                --train                     train optimized HMM model (not recommended to use)
                --test                      test HMM model to identify CNV
                --wgs                       test HMM model to identify CNV from transformed wgs data
                --trio                      posterior CNV calls for father-mother-offspring trio
                --quartet                   posterior CNV calls for quartet
                --joint                     joint CNV calls for trio
                --cctest                    case-control comparison of per-marker CNV frequency
                --validate                  validate copy number at a pre-specified region

            Input/output Files:
                --listfile <file>           a list file containing path to files to be processed
                --output <file>             specify output root filename
                --logfile <file>            write notification/warning messages to this file
                --hmmfile <file>            HMM model file
                --pfbfile <file>            population frequency for B allelel file
                --sexfile <file>            a 2-column file containing filename and sex (male/female) for chrx CNV calling
                --cnvfile <file>            specify CNV call file for use in family-based CNV calling by -trio or -quartet
                --directory <string>        specify the directory where signal files are located
                --refchr <string>           specify a chromosome for wave adjustment (default: 11 for human)
                --refgcfile <file>          a file containing GC percentage of each 1M region of the chromosome specified by --refchr (default: 11 for human)
                --gcmodelfile <file>        a file containing GC model for wave adjustment
                --phenofile <file>          a file containing phenotype information for each input file for -cctest operation

            CNV output control:
                --minsnp <int>              minimum number of SNPs within CNV (default=3)
                --minlength <int>           minimum length of bp within CNV
                --minconf <float>           minimum confidence score of CNV
                --confidence                calculate confidence for each CNV
                --chrx                      use chrX-specific treatment
                --chry                      use chrY-specific treatment (available soon)

            Validation-calling arguments:
                --startsnp <string>         start SNP of a pre-specified region for --validate operation
                --endsnp <string>           end SNP of a pre-specified region for --validate operation
                --delfreq <float>           prior deletion frequency of a pre-specified region for --validate operation
                --dupfreq <float>           prior duplication frequency of a pre-specified region for --validate operation
                --backfreq <float>          background CNV probability for any loci (default: 0.0001)
                --candlist <file>           a file containing all candidate CNV regions to be validated

            Misc options
                --loh                       detect copy-neutral LOH (obselete argument; for SNP arrays only!)
                --exclude_heterosomic       empirically exclude CNVs in heterosomic chromosomes
                --fmprior <numbers>         prior belief on CN state for regions with CNV calls
                --denovo_rate <float>       prior belief on genome-wide de novo event rate (default=0.0001)
                --tabout                    use tab-delimited output
                --coordinate_from_input     get marker coordindate information from input signal file
                --control_label <string>    the phenotype label for control subjects in the phenotype file (default=control)
                --onesided                  performed one-sided test for --cctest operation
                --type_filter <dup|del>     used together with --cctest to specify types of CNVs to be tested
                --(no)medianadjust          adjust genome-wide LRR such that median=0 (default=ON)
                --(no)bafadjust             adjust genome-wide BAF such that median=0.5 (default=ON)
                --(no)sdadjust              adjust SD of hidden Markov model based on input signal (default=ON)
                --(no)flush                 flush input/output buffer (default=ON)
                --bafxhet <float>           minimum BAF het rate to predict female gender when -sexfile is not supplied (default=0.1)

     Function: generate CNV calls from high-density SNP genotyping data that
     contains Log R Ratio and B Allele Frequency for each SNP or CN marker. Use -m
     argument to read the complete manual.

     Example: -test -hmm hhall.hmm -pfb hhall.pfb file1 file2 file3 -log logfile -out outfile
     -trio -hmm hhall.hmm -pfb hhall.pfb -cnv outfile file1 file2 file3
     -validate -hmm hhall.hmm -pfb hhall.pfb -startsnp rs100 -endsnp rs200 -delfreq 0.2 file1 file2 file3

     Version: $LastChangedDate: 2013-02-08 11:10:50 -0800 (Fri, 08 Feb 2013) 
[user@cn0862 ~]$ -h
[user@cn0862 ~]$ -h
[user@cn0862 ~]$ -h  
[user@cn0862 ~]$ -h
[user@cn0862 ~]$ -h
[user@cn0862 ~]$ -h
[user@cn0862 ~]$ -h
[user@cn0862 ~]$ -h
[user@cn0862 ~]$ -h
Exit the application:
[user@cn0862 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$