Package picard.vcf.filter
Class FilterVcf
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.filter.FilterVcf
Applies a set of hard filters to Variants and to Genotypes within a VCF.
-
Field Summary
FieldsModifier and TypeFieldDescriptiondouble
double
int
int
double
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
Field Details
-
INPUT
-
OUTPUT
-
MIN_AB
@Argument(doc="The minimum allele balance acceptable before filtering a site. Allele balance is calculated for heterozygotes as the number of bases supporting the least-represented allele over the total number of base observations. Different heterozygote genotypes at the same locus are measured independently. The locus is filtered if any allele balance is below the limit.") public double MIN_AB -
MIN_DP
@Argument(doc="The minimum sequencing depth supporting a genotype before the genotype will be filtered out.") public int MIN_DP -
MIN_GQ
@Argument(doc="The minimum genotype quality that must be achieved for a sample otherwise the genotype will be filtered out.") public int MIN_GQ -
MAX_FS
@Argument(doc="The maximum phred scaled fisher strand value before a site will be filtered out.") public double MAX_FS -
MIN_QD
@Argument(doc="The minimum QD value to accept or otherwise filter out the variant.") public double MIN_QD -
JAVASCRIPT_FILE
@Argument(shortName="JS", doc="Filters a VCF file with a javascript expression interpreted by the java javascript engine. The script puts the following variables in the script context: \'variant\' a VariantContext ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/variantcontext/VariantContext.html ) and \'header\' a VCFHeader ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/vcf/VCFHeader.html ). Last value of the script should be a boolean to tell whether we should accept or reject the record.", optional=true) public File JAVASCRIPT_FILE
-
-
Constructor Details
-
FilterVcf
public FilterVcf()Constructor to default to having index creation on.
-
-
Method Details
-
doWork
protected int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
-