What it does

This tool runs the samtools depad command in the SAMtools toolkit.

Input is a padded FASTA file (with gaps represented by either * or - characters) and a SAM or BAM file mapped against this padded FASTA file.

The output is a new BAM file mapped against the unpadded FASTA file created by removing all gap characters from the sequence.

Citation

If you use this Galaxy tool in work leading to a scientific publication please cite:

Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16), 2078-9. https://doi.org/10.1093/bioinformatics/btp352

Peter J.A. Cock (2014), Galaxy wrapper for the samtools depad command http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad