samtools provides simple stats on BAM files samtools flagstat "$input1" > "$output1"

**What it does** This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml ------ **Citation** For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*