VerifyIDintensity

verifyIDintensity is a software that detects and estimates sample contamination using intensity data from Illumina genotyping arrays using a mixture model.

Download verifyIDintensity

• GitHub repository

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