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Depad SAM/BAM file (version 0.0.5)

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.


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.

Peter J.A. Cock (2014), Galaxy wrapper for the samtools depad command

This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at