public class LiftoverVcf extends CommandLineProgram
Modifier and Type | Field and Description |
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File |
CHAIN |
static String |
FILTER_CANNOT_LIFTOVER
Filter name to use when a target cannot be lifted over.
|
static String |
FILTER_MISMATCHING_REF_ALLELE
Filter name to use when a target is lifted over, but the reference allele doens't match the new reference.
|
File |
INPUT |
File |
OUTPUT |
File |
REFERENCE_SEQUENCE |
File |
REJECT |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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LiftoverVcf() |
Modifier and Type | Method and Description |
---|---|
protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="O", doc="The output location to write the lifted over VCF/BCF to.") public File OUTPUT
@Option(shortName="C", doc="The liftover chain file. See https://genome.ucsc.edu/goldenPath/help/chain.html for a description of chain files. See http://hgdownload.soe.ucsc.edu/downloads.html#terms for where to download chain files.") public File CHAIN
@Option(shortName="R", common=false, doc="The reference sequence (fasta) for the TARGET genome build. The fasta file must have an accompanying sqeuence dictionary (.dict file).") public File REFERENCE_SEQUENCE
public static final String FILTER_CANNOT_LIFTOVER
public static final String FILTER_MISMATCHING_REF_ALLELE
public static void main(String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram