PicardDuplicateRemoval: The PicardDuplicateRemoval class

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Package: aroma.seq
Class PicardDuplicateRemoval

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--SamTransform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--PicardDuplicateRemoval

Directly known subclasses:

public static class PicardDuplicateRemoval
extends SamTransform

This method flags reads that are aligned to more than one locus, which is done using Picard's 'MarkDuplicates' method [1].

Note that it is assumed that the input BAM files are already sorted, which also means that it can be assumed that the output BAM files are sorted. As with all other methods that outputs BAM files, this methods index all outputted BAM files.

Usage

PicardDuplicateRemoval(..., ASSUME_SORTED=TRUE, VALIDATION_STRINGENCY="SILENT")

Arguments

...	Arguments passed to AromaSeqTransform.
ASSUME_SORTED, VALIDATION_STRINGENCY	Additional arguments passed to Picard MarkDuplicates.

Fields and Methods

Methods:

	getOutputDataSet	-
	process	-

Methods inherited from SamTransform:
getRootPath

Methods inherited from AromaSeqTransform:
as.character, findFilesTodo, getAcronym, getAsteriskTags, getFlavor, getFullName, getInputDataSet, getName, getOptionalArguments, getOrganism, getOutputDataSet, getParameters, getPath, getRootPath, getTags, isDone, length, process, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, findRspReportTemplate, asThis

Benchmarking

As a very rough guideline, a 1.0GB BAM file takes about 10-15 minutes to process using this method.

Author(s)

Henrik Bengtsson

References

[1] Picard, http://picard.sourceforge.net/

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.