Runs Picard's CollectVariantCallingMetrics metrics.
Class to remove a BAM file and also the BAI file if it exists.
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.
Run's Picard's FilterVcf tool to provide hard filtering of variants.
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.
Converts an IntervalList file into a BED file.
Task to run Picard's IntervalListTools.
Task for running MergeSamFiles with one or more inputs.
Runs Picard's MergeVcfs to pull together multiple VCFs with identical sample lists
Simple trait that requires knowing where a metrics file is for a Picard metric generating tool.
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.
Runs Picard's SamToFastq to generate a single fastq or a pair of fastq files from a BAM file.
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.