jvarkit

Biostar84452

remove clipped bases from a BAM file

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar biostar84452  [options] Files

Usage: biostar84452 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    -t, --tag
      tag to flag samrecord as processed
    --version
      print version and exit

Keywords

• sam
• bam
• clip

See also in Biostars

• https://www.biostars.org/p/84452

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar84452.java

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 biostar84452 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Cited In

• Suppl. material of: “The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology”. http://genome.cshlp.org/content/27/11/1916.short Gardner et al. Genome Res. 2017. 27: 1916-1929
• Molly M McDonough, Lillian D Parker, Nancy Rotzel McInerney, Michael G Campana, Jesus E Maldonado; Performance of commonly requested destructive museum samples for mammalian genomic studies, Journal of Mammalogy, , gyy080, https://doi.org/10.1093/jmammal/gyy080
• A long noncoding RNA promotes parasite differentiation in African trypanosomes. Fabien GueganK & al. Sci. Adv., 8 (24), eabn2706. . DOI: 10.1126/sciadv.abn2706
• Baaijens, J.A., Zulli, A., Ott, I.M. et al. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biol 23, 236 (2022). https://doi.org/10.1186/s13059-022-02805-9
• The Mitoribosome. Methods in Molecular Biology. https://doi.org/10.1007/978-1-0716-3171-3

Example

$  java -jar dist/biostar84452.jar samtools-0.1.18/examples/toy.sam > out.sam

@HD	VN:1.4	SO:unsorted
@SQ	SN:ref	LN:45
@SQ	SN:ref2	LN:40
@PG	ID:0	PN:com.github.lindenb.jvarkit.tools.biostar.Biostar84452	VN:b5ebf67dd2926d8a6afadb4d1e36a4959508057f	CL:samtools-0.1.18/examples/toy.sam
(...)
r002	0	ref	9	0	2I6M1P1I1P1I4M2I	*	0	0	AAAGATAAGGGATAAA	*
(...)


$ grep r002 samtools-0.1.18/examples/toy.sam
r002	0	ref	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*

See also

• https://twitter.com/EugenomeUK/status/938031803612491776

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