## Utilities / Count alignments in BAM

### Description

Given a BAM file, this tool counts how many alignments it contains, taking the mapping quality into account if needed.

### Parameters

- Minimum mapping quality required for counting (0-1000) [0]

### Details

By default all alignments are counted, but users can choose to count only alignments which have the specified mapping quality or higher (note that unlike BWA, Bowtie doesn't calculate mapping quality, it just inserts 255 to the field 5 of BAM file if the read aligns, and 0 if it doesn't align).

### Output

Output is a text file containing the number of alignments.

### References

This tool is based on the SAMtools package. Please cite the article The Sequence alignment/map (SAM) format and SAMtools by Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) Bioinformatics, 25, 2078-9. [PMID: 19505943].