Package picard.sam
Class DownsampleSam
- java.lang.Object
-
- picard.cmdline.CommandLineProgram
-
- picard.sam.DownsampleSam
-
@DocumentedFeature public class DownsampleSam extends CommandLineProgram
Summary
This tool applies a downsampling algorithm to a SAM or BAM file to retain only a (deterministically random) subset of the reads. Reads from the same template (e.g. read-pairs, secondary and supplementary reads) are all either kept or discarded as a unit, with the goal of retaining reads fromPROBABILITY * (input templates)
. The results will contain approximatelyPROBABILITY * (input reads)
, however for very small probabilities this may not be the case. A number of different downsampling strategies are supported using theSTRATEGY
option:- ConstantMemory
- Downsamples a stream or file of SAMRecords using a hash-projection strategy such that it can run in constant memory. The downsampling is stochastic, and therefore the actual retained proportion will vary around the requested proportion. Due to working in fixed memory this strategy is good for large inputs, and due to the stochastic nature the accuracy of this strategy is highest with a high number of output records, and diminishes at low output volumes.
- HighAccuracy
- Attempts (but does not guarantee) to provide accuracy up to a specified limit. Accuracy is defined as emitting a proportion of reads as close to the requested proportion as possible. In order to do so this strategy requires memory that is proportional to the number of template names in the incoming stream of reads, and will thus require large amounts of memory when running on large input files.
- Chained
- Attempts to provide a compromise strategy that offers some of the advantages of both the ConstantMemory and HighAccuracy strategies. Uses a ConstantMemory strategy to downsample the incoming stream to approximately the desired proportion, and then a HighAccuracy strategy to finish. Works in a single pass, and will provide accuracy close to (but often not as good as) HighAccuracy while requiring memory proportional to the set of reads emitted from the ConstantMemory strategy to the HighAccuracy strategy. Works well when downsampling large inputs to small proportions (e.g. downsampling hundreds of millions of reads and retaining only 2%. Should be accurate 99.9% of the time when the input contains more than 50,000 templates (read names). For smaller inputs, HighAccuracy is recommended instead.
CollectQualityYieldMetrics.QualityYieldMetrics
metrics file via theMETRICS_FILE
.Usage examples:
Downsample file, keeping about 10% of the reads
java -jar picard.jar DownsampleSam \ I=input.bam \ O=downsampled.bam \ P=0.1
Downsample file, keeping 2% of the reads
java -jar picard.jar DownsampleSam \ I=input.bam \ O=downsampled.bam \ STRATEGY=Chained \ P=0.02 \ ACCURACY=0.0001
Downsample file, keeping 0.001% of the reads (may require more memory)
java -jar picard.jar DownsampleSam \ I=input.bam \ O=downsampled.bam \ STRATEGY=HighAccuracy \ P=0.00001 \ ACCURACY=0.0000001
-
-
Field Summary
Fields Modifier and Type Field Description double
ACCURACY
File
INPUT
File
METRICS_FILE
File
OUTPUT
double
PROBABILITY
Integer
RANDOM_SEED
static String
RANDOM_SEED_TAG
htsjdk.samtools.DownsamplingIteratorFactory.Strategy
STRATEGY
-
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
-
Constructor Summary
Constructors Constructor Description DownsampleSam()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.protected ReferenceArgumentCollection
makeReferenceArgumentCollection()
-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
-
-
-
Field Detail
-
INPUT
@Argument(shortName="I", doc="The input SAM or BAM file to downsample.") public File INPUT
-
OUTPUT
@Argument(shortName="O", doc="The output, downsampled, SAM, BAM or CRAM file to write.") public File OUTPUT
-
STRATEGY
@Argument(shortName="S", doc="The downsampling strategy to use. See usage for discussion.") public htsjdk.samtools.DownsamplingIteratorFactory.Strategy STRATEGY
-
RANDOM_SEED
@Argument(shortName="R", doc="Random seed used for deterministic results. Setting to null will cause multiple invocations to produce different results. The header if the file will be checked for any previous runs of DownsampleSam. If DownsampleSam has been run before on this data with the same seed, the seed will be updated in a deterministic fashion so the DownsampleSam will perform correctly, and still deterministically.") public Integer RANDOM_SEED
-
PROBABILITY
@Argument(shortName="P", doc="The probability of keeping any individual read, between 0 and 1.") public double PROBABILITY
-
ACCURACY
@Argument(shortName="A", doc="The accuracy that the downsampler should try to achieve if the selected strategy supports it. Note that accuracy is never guaranteed, but some strategies will attempt to provide accuracy within the requested bounds.Higher accuracy will generally require more memory.") public double ACCURACY
-
METRICS_FILE
@Argument(shortName="M", doc="The metrics file (of type QualityYieldMetrics) which will contain information about the downsampled file.", optional=true) public File METRICS_FILE
-
RANDOM_SEED_TAG
public static final String RANDOM_SEED_TAG
- See Also:
- Constant Field Values
-
-
Method Detail
-
customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
-
doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
-
makeReferenceArgumentCollection
protected ReferenceArgumentCollection makeReferenceArgumentCollection()
- Overrides:
makeReferenceArgumentCollection
in classCommandLineProgram
-
-