public class LiftoverVcf extends CommandLineProgram
Modifier and Type | Field and Description |
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boolean |
ALLOW_MISSING_FIELDS_IN_HEADER |
java.io.File |
CHAIN |
protected static int |
EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE |
static java.lang.String |
FILTER_CANNOT_LIFTOVER_INDEL
Filter name to use when a target cannot be lifted over.
|
static java.lang.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.
|
static java.lang.String |
FILTER_NO_TARGET
Filter name to use when a target cannot be lifted over.
|
java.io.File |
INPUT |
double |
LIFTOVER_MIN_MATCH |
static java.lang.String |
ORIGINAL_CONTIG
Attribute used to store the name of the source contig/chromosome prior to liftover.
|
static java.lang.String |
ORIGINAL_START
Attribute used to store the position of the variant on the source contig prior to liftover.
|
java.io.File |
OUTPUT |
java.io.File |
REFERENCE_SEQUENCE |
java.io.File |
REJECT |
boolean |
WARN_ON_MISSING_CONTIG |
boolean |
WRITE_ORIGINAL_POSITION |
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.
|
protected static htsjdk.variant.variantcontext.GenotypesContext |
fixGenotypes(htsjdk.variant.variantcontext.GenotypesContext originals,
java.util.Map<htsjdk.variant.variantcontext.Allele,htsjdk.variant.variantcontext.Allele> reverseComplementAlleleMap) |
static void |
main(java.lang.String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="I", doc="The input VCF/BCF file to be lifted over.") public java.io.File INPUT
@Option(shortName="O", doc="The output location to write the lifted over VCF/BCF to.") public java.io.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 java.io.File CHAIN
@Option(shortName="R", common=false, doc="The reference sequence (fasta) for the TARGET genome build. The fasta file must have an accompanying sequence dictionary (.dict file).") public java.io.File REFERENCE_SEQUENCE
@Option(shortName="WMC", doc="Warn on missing contig.", optional=true) public boolean WARN_ON_MISSING_CONTIG
@Option(doc="Write the original contig/position for lifted variants to the INFO field.", optional=true) public boolean WRITE_ORIGINAL_POSITION
@Option(doc="The minimum percent match required for a variant to be lifted.", optional=true) public double LIFTOVER_MIN_MATCH
@Option(doc="Allow INFO and FORMAT in the records that are not found in the header", optional=true) public boolean ALLOW_MISSING_FIELDS_IN_HEADER
protected static int EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE
public static final java.lang.String FILTER_CANNOT_LIFTOVER_INDEL
public static final java.lang.String FILTER_NO_TARGET
public static final java.lang.String FILTER_MISMATCHING_REF_ALLELE
public static final java.lang.String ORIGINAL_CONTIG
public static final java.lang.String ORIGINAL_START
public static void main(java.lang.String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected static htsjdk.variant.variantcontext.GenotypesContext fixGenotypes(htsjdk.variant.variantcontext.GenotypesContext originals, java.util.Map<htsjdk.variant.variantcontext.Allele,htsjdk.variant.variantcontext.Allele> reverseComplementAlleleMap)