Package picard.vcf.MendelianViolations
Class FindMendelianViolations
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.MendelianViolations.FindMendelianViolations
Summary
Finds mendelian violations (MVs) of all types within a VCF.Detail
Takes in VCF or BCF and a pedigree file and looks for high confidence calls where the genotype of the offspring is incompatible with the genotypes of the parents.Key features:
- Checks for regular MVs in diploid regions and invalid transmissions in haploid regions (using the declared gender of the offspring in the pedigree file to determine how to deal with the male and female chromosomes.)
- Outputs metrics about the different kinds of MVs found
- Can output a per-trio VCF with violations; INFO field will indicate the type of violation in the MV field
Example
java -jar picard.jar FindMendelianViolations\\ I=input.vcf \\ TRIO=pedigree.fam \\ O=report.mendelian_violation_metrics \\ MIN_DP=20
Caveates
Assumptions
The tool assumes the existence of FORMAT fields AD, DP, GT, GQ, and PL.Ignored Variants
This tool ignores variants that are:- Not SNPs
- Filtered
- Multiallelic (i.e., trio has more than 2 alleles)
- Within the
SKIP_CHROMS
contigs
PseudoAutosomal Region
This tool assumes that variants in the PAR will be mapped onto the female chromosome, and will treat variants in that region as as autosomal. The mapping to female requires that the PAR in the male chromosome be masked so that the aligner maps reads to single contig. This is normally done for the public releases of the human reference. The tool has default values for PAR that are sensible for humans on either build b37 or hg38.-
Field Summary
FieldsModifier and TypeFieldDescriptionint
int
double
boolean
int
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, 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
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
Field Details
-
INPUT
-
TRIOS
@Argument(shortName="PED", doc="File of Trio information in PED format (with no genotype columns).") public File TRIOS -
OUTPUT
-
MIN_GQ
@Argument(shortName="GQ", doc="Minimum genotyping quality (or non-ref likelihood) to perform tests.") public int MIN_GQ -
MIN_DP
@Argument(shortName="DP", doc="Minimum depth in each sample to consider possible mendelian violations.") public int MIN_DP -
MIN_HET_FRACTION
@Argument(shortName="MINHET", doc="Minimum allele balance at sites that are heterozygous in the offspring.") public double MIN_HET_FRACTION -
VCF_DIR
@Argument(optional=true, doc="If provided, output per-family VCFs of mendelian violations into this directory.") public File VCF_DIR -
SKIP_CHROMS
-
MALE_CHROMS
-
FEMALE_CHROMS
-
PSEUDO_AUTOSOMAL_REGIONS
-
THREAD_COUNT
@Argument(doc="The number of threads that will be used to collect the metrics. ") public int THREAD_COUNT -
TAB_MODE
@Argument(doc="If true then fields need to be delimited by a single tab. If false the delimiter is one or more whitespace characters. Note that tab mode does not strictly follow the PED spec") public boolean TAB_MODE
-
-
Constructor Details
-
FindMendelianViolations
public FindMendelianViolations()
-
-
Method Details
-
customCommandLineValidation
Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable objects to ensure their parsability- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
-
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.
-