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.

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