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
Source code
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