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Sequence logo for different alleles or generated from SAM/BAM


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

Usage: java -jar dist/jvarkit.jar sam4weblogo  [options] Files

Usage: sam4weblogo [options] Files
    -c, --clipped, --clip
      Use Clipped Bases
      Default: false
    --format, -F
      output format.
      Default: fasta
      Possible Values: [fasta, fastq, tabular]
    -fqp, --fqp
      [20180813] fastq padding quality character
      Default: -
    -fqu, --fqu
      [20180813] fastq unknown quality character
      Default: !
    -h, --help
      print help and exit
      What kind of help. One of [usage,markdown,xml].
  * -r, --region, --interval
      Region to observe. 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;,]'
      Default: (unspecified)
      How to print a Read. A format 'a la C-printf'. %% :% , %n:read name, %s: 
      read bases, %q: read quals, %f : read flags,%m: mapq, %c: contig, %b: 
      start, %B: unclipped start, %e: end, %E: unclipped end,%I: read group 
      id, %N: sample name,%S: SAM String.
      Default: %n (%f) %N
      Do not show insertions
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -readFilter, --readFilter
      [20171201](moved to jexl)A JEXL Expression that will be used to filter 
      out some sam-records (see 
      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: 'Accept all' (Empty expression)
    -R, --reference
      For Reading CRAM. Indexed fasta Reference file. This file must be 
      indexed with samtools faidx and with picard/gatk 
      CreateSequenceDictionary or samtools dict
      print version and exit


See also in Biostars

Creation Date


Source code


Unit Tests




The project is licensed under the MIT license.


Should you cite sam4weblogo ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:


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