public class FilterVcf extends CommandLineProgram
Modifier and Type | Field and Description |
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java.io.File |
INPUT |
java.io.File |
JAVASCRIPT_FILE |
double |
MAX_FS |
double |
MIN_AB |
int |
MIN_DP |
int |
MIN_GQ |
double |
MIN_QD |
java.io.File |
OUTPUT |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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FilterVcf()
Constructor to default to having index creation on.
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Modifier and Type | Method and Description |
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protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(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
@Option(doc="The minimum sequencing depth supporting a genotype before the genotype will be filtered out.") public int MIN_DP
@Option(doc="The minimum genotype quality that must be achieved for a sample otherwise the genotype will be filtered out.") public int MIN_GQ
@Option(doc="The maximum phred scaled fisher strand value before a site will be filtered out.") public double MAX_FS
@Option(doc="The minimum QD value to accept or otherwise filter out the variant.") public double MIN_QD
@Option(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 wether we should accept or reject the record.", optional=true) public java.io.File JAVASCRIPT_FILE
public static void main(java.lang.String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram