VerifyIDintensity
verifyIDintensity is a software that detects and estimates sample contamination using intensity data from Illumina genotyping arrays using a mixture model.
Download verifyIDintensity
Build verifyID intensity
To build verifyIDintensity, run the following series of commands. You need boost library and tclap.
$ tar xzvf verifyIDintensity.tgz $ make
Basic Usage
verifyIDintensity [-t <float>] [-m <int>] -n <int> [-b <string>] [-s <string>] -i <string> [-v] [-p] [--] [--version] [-h]
Options
-t <float>, --threshold <float>
Minimum allele frequency for likelihood estimation, default is 0.01
-m <int>, --marker <int>
(required) Number of markers
-n <int>, --number <int>
(required) Number of samples
-b <string>, --abf <string>
Allele frequency file (ABF), which is a plain text file with SNP_ID and Allele_B frequency.
SNP_IDs should be sorted in the same order as the intensity file
-s <string>, --stat <string>
Statistics file (created if not exist)
-i <string>, --in <string>
(required) Input pre-computed intensity (.adpc.bin) file
-v, --verbose
Turn on verbose mode
-p, --persample
Do per-sample analysis, default is per-marker analysis
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
Reference
Please cite the following paper:
G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang, Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data, American journal of human genetics doi:10.1016/j.ajhg.2012.09.004 (volume 91 issue 5 pp.839 - 848)
For sequence data
VerifyBamID software can estimate sample contamination from aligned sequence reads and population minor allele frequency
