| htsjdk.samtools |
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| org.broadinstitute.hellbender |
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| org.broadinstitute.hellbender.cmdline |
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| org.broadinstitute.hellbender.cmdline.argumentcollections |
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| org.broadinstitute.hellbender.cmdline.GATKPlugin |
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| org.broadinstitute.hellbender.cmdline.programgroups |
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| org.broadinstitute.hellbender.engine |
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| org.broadinstitute.hellbender.engine.filters |
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| org.broadinstitute.hellbender.engine.spark |
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| org.broadinstitute.hellbender.engine.spark.datasources |
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| org.broadinstitute.hellbender.exceptions |
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| org.broadinstitute.hellbender.metrics |
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| org.broadinstitute.hellbender.metrics.analysis |
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| org.broadinstitute.hellbender.testutils |
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| org.broadinstitute.hellbender.tools |
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| org.broadinstitute.hellbender.tools.copynumber |
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| org.broadinstitute.hellbender.tools.copynumber.arguments |
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| org.broadinstitute.hellbender.tools.copynumber.caller |
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| org.broadinstitute.hellbender.tools.copynumber.datacollection |
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| org.broadinstitute.hellbender.tools.copynumber.denoising |
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| org.broadinstitute.hellbender.tools.copynumber.formats |
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| org.broadinstitute.hellbender.tools.copynumber.formats.collections |
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| org.broadinstitute.hellbender.tools.copynumber.formats.metadata |
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| org.broadinstitute.hellbender.tools.copynumber.formats.records |
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| org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation |
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| org.broadinstitute.hellbender.tools.copynumber.gcnv |
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| org.broadinstitute.hellbender.tools.copynumber.models |
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| org.broadinstitute.hellbender.tools.copynumber.plotting |
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| org.broadinstitute.hellbender.tools.copynumber.segmentation |
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| org.broadinstitute.hellbender.tools.copynumber.utils |
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| org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval |
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| org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging |
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| org.broadinstitute.hellbender.tools.copynumber.utils.optimization |
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| org.broadinstitute.hellbender.tools.copynumber.utils.segmentation |
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| org.broadinstitute.hellbender.tools.examples |
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| org.broadinstitute.hellbender.tools.examples.metrics.multi |
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| org.broadinstitute.hellbender.tools.examples.metrics.single |
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| org.broadinstitute.hellbender.tools.funcotator |
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| org.broadinstitute.hellbender.tools.funcotator.compositeoutput |
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| org.broadinstitute.hellbender.tools.funcotator.dataSources |
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| org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic |
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| org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode |
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| org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment |
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| org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf |
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| org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv |
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| org.broadinstitute.hellbender.tools.funcotator.filtrationRules |
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| org.broadinstitute.hellbender.tools.funcotator.genelistoutput |
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| org.broadinstitute.hellbender.tools.funcotator.mafOutput |
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| org.broadinstitute.hellbender.tools.funcotator.metadata |
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| org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput |
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| org.broadinstitute.hellbender.tools.funcotator.vcfOutput |
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| org.broadinstitute.hellbender.tools.genomicsdb |
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| org.broadinstitute.hellbender.tools.readersplitters |
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| org.broadinstitute.hellbender.tools.spark |
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| org.broadinstitute.hellbender.tools.spark.bwa |
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| org.broadinstitute.hellbender.tools.spark.pathseq |
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| org.broadinstitute.hellbender.tools.spark.pathseq.loggers |
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| org.broadinstitute.hellbender.tools.spark.pipelines |
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| org.broadinstitute.hellbender.tools.spark.pipelines.metrics |
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| org.broadinstitute.hellbender.tools.spark.sv |
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| org.broadinstitute.hellbender.tools.spark.sv.discovery |
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| org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment |
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| org.broadinstitute.hellbender.tools.spark.sv.discovery.inference |
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| org.broadinstitute.hellbender.tools.spark.sv.evidence |
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| org.broadinstitute.hellbender.tools.spark.sv.utils |
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| org.broadinstitute.hellbender.tools.spark.transforms |
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| org.broadinstitute.hellbender.tools.spark.transforms.markduplicates |
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| org.broadinstitute.hellbender.tools.spark.utils |
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| org.broadinstitute.hellbender.tools.spark.validation |
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| org.broadinstitute.hellbender.tools.validation |
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| org.broadinstitute.hellbender.tools.walkers |
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| org.broadinstitute.hellbender.tools.walkers.annotator |
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| org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific |
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| org.broadinstitute.hellbender.tools.walkers.bqsr |
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| org.broadinstitute.hellbender.tools.walkers.consensus |
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| org.broadinstitute.hellbender.tools.walkers.contamination |
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| org.broadinstitute.hellbender.tools.walkers.coverage |
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| org.broadinstitute.hellbender.tools.walkers.fasta |
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| org.broadinstitute.hellbender.tools.walkers.filters |
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| org.broadinstitute.hellbender.tools.walkers.genotyper |
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| org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc |
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| org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper |
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| org.broadinstitute.hellbender.tools.walkers.haplotypecaller |
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| org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs |
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| org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading |
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| org.broadinstitute.hellbender.tools.walkers.mutect |
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| org.broadinstitute.hellbender.tools.walkers.mutect.clustering |
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| org.broadinstitute.hellbender.tools.walkers.mutect.filtering |
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| org.broadinstitute.hellbender.tools.walkers.qc |
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| org.broadinstitute.hellbender.tools.walkers.readorientation |
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| org.broadinstitute.hellbender.tools.walkers.realignmentfilter |
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| org.broadinstitute.hellbender.tools.walkers.rnaseq |
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| org.broadinstitute.hellbender.tools.walkers.sv |
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| org.broadinstitute.hellbender.tools.walkers.validation |
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| org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup |
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| org.broadinstitute.hellbender.tools.walkers.varianteval |
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| org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators |
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| org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications |
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| org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager |
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| org.broadinstitute.hellbender.tools.walkers.varianteval.util |
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| org.broadinstitute.hellbender.tools.walkers.variantutils |
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| org.broadinstitute.hellbender.tools.walkers.vqsr |
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| org.broadinstitute.hellbender.transformers |
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| org.broadinstitute.hellbender.utils |
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| org.broadinstitute.hellbender.utils.activityprofile |
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| org.broadinstitute.hellbender.utils.artifacts |
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| org.broadinstitute.hellbender.utils.baq |
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| org.broadinstitute.hellbender.utils.bwa |
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| org.broadinstitute.hellbender.utils.clipping |
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| org.broadinstitute.hellbender.utils.codecs |
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| org.broadinstitute.hellbender.utils.codecs.copynumber |
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| org.broadinstitute.hellbender.utils.codecs.gtf |
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| org.broadinstitute.hellbender.utils.codecs.refseq |
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| org.broadinstitute.hellbender.utils.codecs.sampileup |
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| org.broadinstitute.hellbender.utils.codecs.table |
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| org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable |
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| org.broadinstitute.hellbender.utils.collections |
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| org.broadinstitute.hellbender.utils.config |
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| org.broadinstitute.hellbender.utils.downsampling |
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| org.broadinstitute.hellbender.utils.fasta |
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| org.broadinstitute.hellbender.utils.fragments |
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| org.broadinstitute.hellbender.utils.functional |
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| org.broadinstitute.hellbender.utils.gcs |
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| org.broadinstitute.hellbender.utils.genotyper |
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| org.broadinstitute.hellbender.utils.haplotype |
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| org.broadinstitute.hellbender.utils.help |
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| org.broadinstitute.hellbender.utils.hmm |
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| org.broadinstitute.hellbender.utils.illumina |
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| org.broadinstitute.hellbender.utils.io |
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| org.broadinstitute.hellbender.utils.iterators |
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| org.broadinstitute.hellbender.utils.locusiterator |
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| org.broadinstitute.hellbender.utils.logging |
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| org.broadinstitute.hellbender.utils.mcmc |
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| org.broadinstitute.hellbender.utils.nio |
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| org.broadinstitute.hellbender.utils.pairhmm |
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| org.broadinstitute.hellbender.utils.param |
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| org.broadinstitute.hellbender.utils.pileup |
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| org.broadinstitute.hellbender.utils.python |
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| org.broadinstitute.hellbender.utils.R |
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| org.broadinstitute.hellbender.utils.read |
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| org.broadinstitute.hellbender.utils.read.markduplicates |
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| org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords |
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| org.broadinstitute.hellbender.utils.read.mergealignment |
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| org.broadinstitute.hellbender.utils.recalibration |
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| org.broadinstitute.hellbender.utils.recalibration.covariates |
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| org.broadinstitute.hellbender.utils.reference |
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| org.broadinstitute.hellbender.utils.report |
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| org.broadinstitute.hellbender.utils.runtime |
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| org.broadinstitute.hellbender.utils.samples |
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| org.broadinstitute.hellbender.utils.smithwaterman |
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| org.broadinstitute.hellbender.utils.solver |
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| org.broadinstitute.hellbender.utils.spark |
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| org.broadinstitute.hellbender.utils.svd |
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| org.broadinstitute.hellbender.utils.text |
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| org.broadinstitute.hellbender.utils.tsv |
Utility classes to read and write tab separated value (tsv) files.
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| org.broadinstitute.hellbender.utils.variant |
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| org.broadinstitute.hellbender.utils.variant.writers |
|
| picard |
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| picard.analysis |
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| picard.analysis.artifacts |
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| picard.analysis.directed |
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| picard.analysis.replicates |
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| picard.annotation |
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| picard.arrays |
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| picard.arrays.illumina |
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| picard.cmdline |
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| picard.cmdline.argumentcollections |
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| picard.cmdline.programgroups |
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| picard.fastq |
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| picard.filter |
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| picard.fingerprint |
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| picard.illumina |
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| picard.illumina.parser |
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| picard.illumina.parser.fakers |
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| picard.illumina.parser.readers |
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| picard.illumina.quality |
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| picard.metrics |
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| picard.nio |
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| picard.pedigree |
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| picard.reference |
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| picard.sam |
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| picard.sam.markduplicates |
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| picard.sam.markduplicates.util |
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| picard.sam.SamErrorMetric |
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| picard.sam.util |
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| picard.util |
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| picard.util.help |
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| picard.util.IntervalList |
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| picard.vcf |
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| picard.vcf.filter |
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| picard.vcf.MendelianViolations |
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| picard.vcf.processor |
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| picard.vcf.processor.util |
|