## Utilities / Retrieve unique alignments from BAM

### Description

Given a BAM file, this tool retrieves unique alignments.

### Parameters

Does the alignment file contain paired-end data (yes, no) [no]

### Details

This tool filters out unaligned reads and alignments which have a mapping quality less than 4. For paired end data it keeps only reads which are mapped in a proper pair.

### Output

Output is a BAM file where each read has the tag NH:i:1 (this tag is used by tools which count RNA-seq reads per genes/exons).

### 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].