This is a copy of an applet created by DNAnexus, which implements the Pindel tool (version 0.2.5a7) for detection of structural variants (large deletions, medium sized insertions, inversions, tandem duplications, etc). The original app (project-BZqK8kQ0Jz1ZQ8KKpbKbqVjv:applet-BZvg6vj0kJxBxXq479vz19YY) was created to support development of Parliament (https://platform.dnanexus.com/panx/projects/BZqK8kQ0Jz1ZQ8KKpbKbqVjv/settings)

The following is the Readme as provided by DNAnexus and links are now out of date. Use https://github.com/genome/pindel/ instead.

Pindel finds breakpoints for deletions, insertions, inversions, and duplications. It detects these on a base pair level.

This app can be run on whole genome or whole exome data to try and find base pair level calls for structural variants.

This app requires an input file containing the mappings and a reference genome in fasta format (*.fa).

This app must have one of the following input combinations or it will raise an AppError:

1. BAM file(s) with extension '.bam' from BWA/MOSAIK AND BAM config file (as specied at http://gmt.genome.wustl.edu/pindel/0.2.4/user-manual.html) OR insert size
2. BAM file(s) with extension '.bam' not from BWA/MOSAIK AND bam_not_produced_by_bwa=True (default=False) AND sequence_platform AND insert size
3. Pindel input file (as specified at http://gmt.genome.wustl.edu/pindel/0.2.4/user-manual.html)

This app outputs 6 files which each contain a different piece of structural variation information.

A _BP file which contains breakpoints not assigned to any event. A _D file which contains deletions. A _INV file which contains inversions. A _LI file which contains long insertions. A _SI file which contains short insertions. A _TD file which contains tandem duplications

This app can also output a VCF containing some of the structural variant information. Because the app includes the reads in its file, the files can become very large.

This app uses a pattern growth approach to find the breaakpoints of variants from paired-end short reads.

For more informatoin, consult the Pindel website at:

http://gmt.genome.wustl.edu/pindel/0.2.4/index.html