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[[Category:Software|VerifyIDintensity]]
'''verifyIDintensity''' is a software that detects and estimates sample contamination using intensity data from Illumina genotyping arrays using a mixture model.
== Download verifyIDintensity ==
* [[File:VerifyIDintensity.tgz]]
== Build verifyID intensity ==
To build verifyIDintensity, run the following series of commands. You need [http://www.boost.org/ boost library] and [http://tclap.sourceforge.net/ 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.
'''verifyIDintensity''' is a software that detects and estimates sample contamination using intensity data from Illumina genotyping arrays using a mixture model.
== Download verifyIDintensity ==
* [[File:VerifyIDintensity.tgz]]
== Build verifyID intensity ==
To build verifyIDintensity, run the following series of commands. You need [http://www.boost.org/ boost library] and [http://tclap.sourceforge.net/ 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.
