picard

Type Members

class CleanSam extends PicardTask with Pipe[SamOrBam, SamOrBam]
class CollectAlignmentSummaryMetrics extends PicardTask with PicardMetricsTask
class CollectGcBiasMetrics extends PicardTask with PicardMetricsTask
class CollectHsMetrics extends PicardTask with PicardMetricsTask
class CollectInsertSizeMetrics extends PicardTask with PicardMetricsTask
class CollectMultipleMetrics extends PicardTask with PicardMetricsTask
class CollectSequencingArtifactMetrics extends PicardTask with PicardMetricsTask
class CollectTargetedPcrMetrics extends PicardTask with PicardMetricsTask
class CollectVariantCallingMetrics extends PicardTask with VariableResources

Runs Picard's CollectVariantCallingMetrics metrics.
class CollectWgsMetrics extends PicardTask with PicardMetricsTask
class CopyBaiToBamBai extends ShellCommand
class DeleteBam extends SimpleInJvmTask

Class to remove a BAM file and also the BAI file if it exists.
Class to remove a BAM file and also the BAI file if it exists. Succeeds if the files can be deleted, *or* if no files were present to be deleted.
class DownsampleSam extends PicardTask

Constructs a new DownsampleSam task.
Constructs a new DownsampleSam task. If 'strategy' is not supplied then a heuristic is used to determine an appropriate strategy and amount of memory to be used. If 'strategy' is supplied then the caller should specify an appropriate Memory resource level.
class EstimateLibraryComplexity extends PicardTask with PicardMetricsTask
class FastqToSam extends PicardTask with Pipe[Fastq, SamOrBam]
class FifoBuffer[A] extends PicardTask with Pipe[A, A]
class FilterVcf extends PicardTask with Pipe[Vcf, Vcf]

Run's Picard's FilterVcf tool to provide hard filtering of variants.
class FixMateInformation extends PicardTask with Pipe[SamOrBam, SamOrBam]
class GatherBamFiles extends PicardTask
class GatherVcfs extends PicardTask
class GenotypeConcordance extends PicardTask

Runs Picard's GenotypeConcordance to assess various variant calling metrics against truth.
Runs Picard's GenotypeConcordance to assess various variant calling metrics against truth.
Please note MISSING_SITES_HOM_REF is set to true by default, whereas the default in GenotypeConcordance is false.
class IntervalListToBed extends PicardTask

Converts an IntervalList file into a BED file.
class IntervalListTools extends PicardTask

Task to run Picard's IntervalListTools.
class MarkDuplicates extends PicardTask with PicardMetricsTask

Note: if no prefix is given, the metrics file will be named based on the first BAM in inputs.
class MarkIlluminaAdapters extends PicardTask with PicardMetricsTask with Pipe[SamOrBam, SamOrBam]
class MergeBamAlignment extends PicardTask with Pipe[SamOrBam, SamOrBam]
class MergeSamFiles extends PicardTask

Task for running MergeSamFiles with one or more inputs.
class MergeVcfs extends PicardTask with PipeOut[Vcf]

Runs Picard's MergeVcfs to pull together multiple VCFs with identical sample lists
trait PicardMetricsTask extends AnyRef

Simple trait that requires knowing where a metrics file is for a Picard metric generating tool.
abstract class PicardTask extends ProcessTask with JarTask with FixedResources with Configuration

Simple class to run any Picard command.
Simple class to run any Picard command. Specific Picard command classes should extend this. Since the order of args is important to a task, an sub-class should call getPicardArgs before adding any tasks to args, and then call super.getTasks if getTasks is overriden.
class RevertSam extends PicardTask
class SamToFastq extends PicardTask with Pipe[SamOrBam, Fastq]

Runs Picard's SamToFastq to generate a single fastq or a pair of fastq files from a BAM file.
class SetNmAndUqTags extends PicardTask with Pipe[SamOrBam, SamOrBam]
class SortSam extends PicardTask with Pipe[SamOrBam, SamOrBam]
class SortVcf extends PicardTask with Pipe[Vcf, Vcf]
class UpdateVcfSequenceDictionary extends PicardTask with Pipe[Vcf, Vcf]
class ValidateSamFile extends PicardTask with PicardMetricsTask

Value Members

object CollectAlignmentSummaryMetrics
object CollectGcBiasMetrics
object CollectHsMetrics
object CollectInsertSizeMetrics
object CollectTargetedPcrMetrics
object CollectWgsMetrics
object DownsamplingStrategy extends Enumeration
object EstimateLibraryComplexity
object FastqToUnmappedSam
object MarkDuplicates
object MarkIlluminaAdapters
object PicardOutput extends Enumeration
object PicardTask
object RevertSam
object SamToFastq
object ValidateSamFile

package picard

Type Members

class CleanSam extends PicardTask with Pipe[SamOrBam, SamOrBam]

class CollectAlignmentSummaryMetrics extends PicardTask with PicardMetricsTask

class CollectGcBiasMetrics extends PicardTask with PicardMetricsTask

class CollectHsMetrics extends PicardTask with PicardMetricsTask

class CollectInsertSizeMetrics extends PicardTask with PicardMetricsTask

class CollectMultipleMetrics extends PicardTask with PicardMetricsTask

class CollectSequencingArtifactMetrics extends PicardTask with PicardMetricsTask

class CollectTargetedPcrMetrics extends PicardTask with PicardMetricsTask

class CollectVariantCallingMetrics extends PicardTask with VariableResources

class CollectWgsMetrics extends PicardTask with PicardMetricsTask

class CopyBaiToBamBai extends ShellCommand

class DeleteBam extends SimpleInJvmTask

class DownsampleSam extends PicardTask

class EstimateLibraryComplexity extends PicardTask with PicardMetricsTask

class FastqToSam extends PicardTask with Pipe[Fastq, SamOrBam]

class FifoBuffer[A] extends PicardTask with Pipe[A, A]

class FilterVcf extends PicardTask with Pipe[Vcf, Vcf]

class FixMateInformation extends PicardTask with Pipe[SamOrBam, SamOrBam]

class GatherBamFiles extends PicardTask

class GatherVcfs extends PicardTask

class GenotypeConcordance extends PicardTask

class IntervalListToBed extends PicardTask

class IntervalListTools extends PicardTask

class MarkDuplicates extends PicardTask with PicardMetricsTask

class MarkIlluminaAdapters extends PicardTask with PicardMetricsTask with Pipe[SamOrBam, SamOrBam]

class MergeBamAlignment extends PicardTask with Pipe[SamOrBam, SamOrBam]

class MergeSamFiles extends PicardTask

class MergeVcfs extends PicardTask with PipeOut[Vcf]

trait PicardMetricsTask extends AnyRef

abstract class PicardTask extends ProcessTask with JarTask with FixedResources with Configuration

class RevertSam extends PicardTask

class SamToFastq extends PicardTask with Pipe[SamOrBam, Fastq]

class SetNmAndUqTags extends PicardTask with Pipe[SamOrBam, SamOrBam]

class SortSam extends PicardTask with Pipe[SamOrBam, SamOrBam]

class SortVcf extends PicardTask with Pipe[Vcf, Vcf]

class UpdateVcfSequenceDictionary extends PicardTask with Pipe[Vcf, Vcf]

class ValidateSamFile extends PicardTask with PicardMetricsTask

Value Members

object CollectAlignmentSummaryMetrics

object CollectGcBiasMetrics

object CollectHsMetrics

object CollectInsertSizeMetrics

object CollectTargetedPcrMetrics

object CollectWgsMetrics

object DownsamplingStrategy extends Enumeration

object EstimateLibraryComplexity

object FastqToUnmappedSam

object MarkDuplicates

object MarkIlluminaAdapters

object PicardOutput extends Enumeration

object PicardTask

object RevertSam

object SamToFastq

object ValidateSamFile

Ungrouped