BamStats05

Last commit

Coverage statistics for a BED file, group by gene

Usage

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

Usage: java -jar dist/jvarkit.jar bamstats05  [options] Files

Usage: bamstats05 [options] Files
  Options:
  * -B, --bed
      bed file (columns: chrom(tab)start(tab)end(tab)GENE)
    -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: record.getMappingQuality()<1 || record.getDuplicateReadFlag() || record.getReadFailsVendorQualityCheckFlag() || record.isSecondaryOrSupplementary()
    --groupby
      Group Reads by. Data partitioning using the SAM Read Group (see 
      https://gatkforums.broadinstitute.org/gatk/discussion/6472/ ) . It can 
      be any combination of sample, library....
      Default: sample
      Possible Values: [readgroup, sample, library, platform, center, sample_by_platform, sample_by_center, sample_by_platform_by_center, any]
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --mapq
      Min mapping quality
      Default: 1
    -merge, --merge
      [20181122] Merge overlapping intervals for the same gene.
      Default: false
    -m, --mincoverage
      Coverage treshold. Any depth under this value will be considered as 
      'not-covered'.  Default: 0
      Default: []
    -o, --output
      Output file. Optional . Default: stdout
    -R, --reference
      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
    --version
      print version and exit

Keywords

  • bam
  • coverage
  • statistics
  • bed

See also in Biostars

Creation Date

20151012

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bamstats04/BamStats05.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/bamstats04/BamStats05Test.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite bamstats05 ? 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

Input

input is one or more indexed bam file.

One file with the suffix '.list' is interpreted as a text file with one path per line.

If there is no argument, stdin is interpreted as a list of path to the bam like in find . -name "*.bam"

Cited In:

  • "Custom hereditary breast cancer gene panel selectively amplifies target genes for reliable variant calling" . BioRxiv https://doi.org/10.1101/322180
  • "Future MicrobiologyVol. 15, No. 15 Comparative genomics of Sporothrix species and identification of putative pathogenic-gene determinants. Published Online:12 Nov 2020https://doi.org/10.2217/fmb-2019-0302"
  • "Key innovation triggers widespread radiation of the genus Medicago". Zhipeng Liu & al. https://doi.org/10.21203/rs.3.rs-3181566/v1
  • Over-expression and increased copy numbers of a cytochrome P450 and two UDP-glucuronosyltransferase genes in macrocyclic lactone resistant Psoroptes ovis of cattle Jack Hearn, Wouter van Mol, Roel Meyermans, Kathryn Bartley, Tyler Alioto, Jessica Gomez-Garrido, Fernando Cruz, Francisco Camara Ferreira, Marta Gut, Ivo Gut, Nadine Buys, Steven Janssens, Karyn Adams, Sara Roose, Thomas Van Leeuwen, Wannes Dermauw, John S. Gilleard, Russell Avramenko, Peter Geldhof, Edwin Claerebout, Stewart T.G. Burgess bioRxiv 2025.02.06.636820; doi: https://doi.org/10.1101/2025.02.06.636820

Example

$ head genes.bed
1   179655424   179655582   ZORG
1   179656788   179656934   ZORG

$ java -jar  dist/bamstats05.jar -B genes.bed --mincoverage 10 in.bam > out.txt

$ head out.txt
#chrom  start   end gene    sample  length  mincov  maxcov  avg nocoverage.bp   percentcovered
1   179655424   179656934   ZORG    SAMPLE1 304 27  405 216.80921052631578  0   100