## Count alignment statistics for BAM

### Description

Given a BAM file, this tool counts statistics for alignments.

### Parameters

None

### Details

Counts statistics for alignments in a BAM file. This tool is based on the SAMtools flagstat tool.

### Output

Output is a txt file containing the statistics.

### 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].