GenerateHaploidCNVGenotypes documentation
GenerateHaploidCNVGenotypes
The GenerateHaploidCNVGenotypes utility converts disploid copy number calls (as generated by the Genome STRiP CNV genotyping) into genotype likelihoods for a set of haploid copy number structural alleles.
Example
java -Xmx4g -cp SVToolkit.jar:GenomeAnalysisTK.jar \ org.broadinstitute.sv.apps.GenerateHaploidCNVGenotypes \ -R reference.fasta \ -ploidyMapFile ploidy_map_file.txt \ -genderMapFile gender_map_file.txt \ -vcf input.genotypes.vcf \ -O output.haploid.genotypes.vcf \ -estimateAlleleFrequencies true \ -genotypeLikelihoodThreshold 0.001
GenerateHaploidCNVGenotypes specific arguments
Name | Type | Default value | Summary |
---|---|---|---|
Required Inputs | |||
-vcf | File | NA | Input file (vcf) |
Required Outputs | |||
-O | File | NA | Output file (vcf) |
Required Parameters | |||
-R | File | NA | Reference fasta file |
Optional Outputs | |||
-log | String | NA | Set the logging location |
Optional Parameters | |||
-debug | String | NA | Print extra debugging output |
-estimateAlleleFrequencies | String | NA | Whether to estimate and use population-based frequency priors at diploid sites (default true) |
-genderMapFile | List[File] | NA | Map file or files containing the gender for each sample |
-genotypeLikelihoodThreshold | double | 0.0 | Threshold at which to consider a copy number class as possible (default zero) |
-l | String | INFO | Set the minimum level of logging |
-ploidyMapFile | File | NA | Ploidy map specifying gender-dependent ploidy for each region of the reference |
-populationMapFile | List[File] | NA | Map file or files containing the assigned population for each sample |
-site | List[String] | NA | List (or .list file) of CNV sites to be included in the output |
-verbose | String | NA | Enable verbose output |
Optional Flags | |||
-h | Flag | NA | Generate the help message |
-version | Flag | NA | Output version information |
Argument details
--debug / -debug ( String )
Print extra debugging output.
--estimateAlleleFrequencies / -estimateAlleleFrequencies ( String )
Whether to estimate and use population-based frequency priors at diploid sites (default true).
--genderMapFile / -genderMapFile ( List[File] )
Map file or files containing the gender for each sample.
--genotypeLikelihoodThreshold / -genotypeLikelihoodThreshold ( double with default value 0.0 )
Threshold at which to consider a copy number class as possible (default zero).
--help / -h ( Flag )
Generate the help message.
--log_to_file / -log ( String )
Set the logging location.
--logging_level / -l ( String with default value INFO )
Set the minimum level of logging.
--outputFile / -O ( required File )
Output file (vcf).
--ploidyMapFile / -ploidyMapFile ( File )
Ploidy map specifying gender-dependent ploidy for each region of the reference.
--populationMapFile / -populationMapFile ( List[File] )
Map file or files containing the assigned population for each sample.
--referenceFile / -R ( required File )
Reference fasta file.
--site / -site ( List[String] )
List (or .list file) of CNV sites to be included in the output.
--vcfFile / -vcf ( required File )
Input file (vcf).
--verbose / -verbose ( String )
Enable verbose output.
--version / -version ( Flag )
Output version information.