jvarkit

BamStats05

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

• https://www.biostars.org/p/324639
• https://www.biostars.org/p/194393
• https://www.biostars.org/p/35083

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

• 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 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

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

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