public class FindMendelianViolations extends CommandLineProgram
Modifier and Type | Field and Description |
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Set<String> |
FEMALE_CHROMS |
File |
INPUT |
Set<String> |
MALE_CHROMS |
int |
MIN_DP |
int |
MIN_GQ |
double |
MIN_HET_FRACTION |
File |
OUTPUT |
Set<String> |
PSEUDO_AUTOSOMAL_REGIONS |
Set<String> |
SKIP_CHROMS |
boolean |
TAB_MODE |
int |
THREAD_COUNT |
File |
TRIOS |
File |
VCF_DIR |
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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FindMendelianViolations() |
Modifier and Type | Method and Description |
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protected String[] |
customCommandLineValidation()
Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable
objects to ensure their parsability
|
protected int |
doWork()
Do the work after command line has been parsed.
|
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="PED", doc="File of Trio information in PED format (with no genotype columns).") public File TRIOS
@Option(shortName="GQ", doc="Minimum genotyping quality (or non-ref likelihood) to perform tests.") public int MIN_GQ
@Option(shortName="DP", doc="Minimum depth in each sample to consider possible mendelian violations.") public int MIN_DP
@Option(shortName="MINHET", doc="Minimum allele balance at sites that are heterozygous in the offspring.") public double MIN_HET_FRACTION
@Option(optional=true, doc="If provided, output per-family VCFs of mendelian violations into this directory.") public File VCF_DIR
@Option(doc="List of chromosome names to skip entirely.") public Set<String> SKIP_CHROMS
@Option(doc="List of possible names for male sex chromosome(s)") public Set<String> MALE_CHROMS
@Option(doc="List of possible names for female sex chromosome(s)") public Set<String> FEMALE_CHROMS
@Option(doc="List of chr:start-end for pseudo-autosomal regions on the female sex chromosome. Defaults to HG19/b37 & HG38 coordinates.") public Set<String> PSEUDO_AUTOSOMAL_REGIONS
@Option(doc="The number of threads that will be used to collect the metrics. ") public int THREAD_COUNT
protected String[] customCommandLineValidation()
customCommandLineValidation
in class CommandLineProgram
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram