picard.fingerprint

Class CheckFingerprint

java.lang.Object

picard.cmdline.CommandLineProgram

picard.fingerprint.CheckFingerprint

public class CheckFingerprint
extends CommandLineProgram

Attempts to check the sample identity of the sequence data in the provided SAM/BAM file against a set of known genotypes in the supplied genotype file (in either GELI or VCF format).

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	DETAIL_OUTPUT
static java.lang.String	FINGERPRINT_DETAIL_FILE_SUFFIX
static java.lang.String	FINGERPRINT_SUMMARY_FILE_SUFFIX
double	GENOTYPE_LOD_THRESHOLD
java.io.File	GENOTYPES
java.io.File	HAPLOTYPE_MAP
boolean	IGNORE_READ_GROUPS
java.io.File	INPUT
java.lang.String	OUTPUT
java.lang.String	SAMPLE_ALIAS
java.io.File	SUMMARY_OUTPUT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CheckFingerprint()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Option(shortName="I",
        doc="Input SAM or BAM file.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="The base of output files to write.  The summary metrics will have the file extension \'fingerprinting_summary_metrics\' and the detail metrics will have the extension \'fingerprinting_detail_metrics\'.",
        mutex={"SUMMARY_OUTPUT","DETAIL_OUTPUT"})
public java.lang.String OUTPUT

SUMMARY_OUTPUT

@Option(shortName="S",
        doc="The text file to which to write summary metrics.",
        mutex="OUTPUT")
public java.io.File SUMMARY_OUTPUT

DETAIL_OUTPUT

@Option(shortName="D",
        doc="The text file to which to write detail metrics.",
        mutex="OUTPUT")
public java.io.File DETAIL_OUTPUT

GENOTYPES

@Option(shortName="G",
        doc="File of genotypes (VCF or GELI) to be used in comparison. May contain any number of genotypes; CheckFingerprint will use only those that are usable for fingerprinting.")
public java.io.File GENOTYPES

SAMPLE_ALIAS

@Option(optional=true,
        doc="If using VCF format genotypes, this parameter can be used to specify which sample\'s genotypes to use from the VCF file.  If not supplied the sample name from the BAM read group header is used instead.")
public java.lang.String SAMPLE_ALIAS

HAPLOTYPE_MAP

@Option(shortName="H",
        doc="A file of haplotype information produced by the CheckFingerprint program.")
public java.io.File HAPLOTYPE_MAP

GENOTYPE_LOD_THRESHOLD

@Option(shortName="LOD",
        doc="When counting haplotypes checked and matching, count only haplotypes where the most likely haplotype achieves at least this LOD.")
public double GENOTYPE_LOD_THRESHOLD

IGNORE_READ_GROUPS

@Option(shortName="IGNORE_RG",
        doc="If true, treat the entire input BAM as one single read group in the calculation, ignoring RG annotations, and producing a single fingerprint metric for the entire BAM.")
public boolean IGNORE_READ_GROUPS

FINGERPRINT_SUMMARY_FILE_SUFFIX

public static final java.lang.String FINGERPRINT_SUMMARY_FILE_SUFFIX

See Also:

Constant Field Values

FINGERPRINT_DETAIL_FILE_SUFFIX

public static final java.lang.String FINGERPRINT_DETAIL_FILE_SUFFIX

See Also:

Constant Field Values

Constructor Detail

CheckFingerprint

public CheckFingerprint()

Method Detail

main

public static void main(java.lang.String[] args)

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 class CommandLineProgram

Returns:

program exit status.