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, --out
      Output file. Optional . Default: stdout
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --regions
      Limit analysis to this interval. A source of intervals. The following 
      suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz, 
      gtf.gz.Otherwise it could be an empty string (no interval) or a list of 
      plain interval separated by '[ \t\n;,]'
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    -t, --tag
      tag to flag samrecord as processed
    --validation-stringency
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --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
• Makamure, C.E., Justinen, S., Martínez, D.E. et al. Cool temperature inhibits binary fission and results in phenotypic and transcriptomic changes that suggest inducible aging in Diadumene lineata. BMC Res Notes 18, 293 (2025). https://doi.org/10.1186/s13104-025-07378-x

Example

$  java -jar dist/jvarkit.jar biostar84452 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