What it does
This tool runs the command samtools view from the SAMtools toolkit, getting all the reads in your BAM file mapped to the given region of interest (ROI). It then counts all the different sequence variants in reads spanning that ROI, which are returned as a tab-separated table.
Reads mapped to the ROI but not spanning it completely are ignored.
Input is a sorted and indexed BAM file, the output is tabular. The first column is the observed sequence variants within the ROI, the second column is the number of reads with that sequence, and the third column gives this as a percentage of the reads spanning the ROI.
| Column | Description |
| 1 | Sequence variant from ROI |
| 2 | Number of reads with that sequence variant |
| 3 | Percentage of reads with that sequence variant (2 dp) |
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 (2016), Count sequence variants in region of interest in BAM file. http://toolshed.g2.bx.psu.edu/view/peterjc/count_roi_variants
This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/count_roi_variants