Biostar145820
subsample/shuffle BAM to fixed number of alignments.
Usage
This program is now part of the main jvarkit
tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar biostar145820 [options] Files
Usage: biostar145820 [options] Files
Options:
--bamcompression
Compression Level. 0: no compression. 9: max compression;
Default: 5
-f, --filter, --jexl
A JEXL Expression that will be used to filter out some sam-records (see
https://software.broadinstitute.org/gatk/documentation/article.php?id=1255).
An expression should return a boolean value (true=exclude, false=keep
the read). An empty expression keeps everything. The variable 'record'
is the current observed read, an instance of SAMRecord (https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html).
Default: 'Accept all' (Empty expression)
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--maxRecordsInRam
When writing files that need to be sorted, this will specify the number
of records stored in RAM before spilling to disk. Increasing this number
reduces the number of file handles needed to sort a file, and increases
the amount of RAM needed
Default: 50000
-o, --output
Output file. Optional . Default: stdout
--reference, -R
For reading/writing CRAM files. Indexed fasta Reference file. This file
must be indexed with samtools faidx and with picard/gatk
CreateSequenceDictionary or samtools dict
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--seed
Random seed. -1 == current time
Default: -1
--tmpDir
tmp working directory. Default: java.io.tmpDir
Default: []
--version
print version and exit
-n
number of reads. negative: all reads, shuffle output.
Default: -1
Keywords
- sam
- bam
- shuffle
See also in Biostars
Creation Date
20150615
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite biostar145820 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
- MED25 connects enhancer-promoter looping and MYC2-dependent activation of jasmonate signalling. Wang et al. Nature Plants 5, 616-625 (2019) https://doi.org/10.1038/s41477-019-0441-9
Example
$ java -jar dist/biostar145820.jar -n 10 -o out.bam in.bam