83 citations
16 runs

bamtools stats

By Barnett D., Marth G., Last update 1494698999
All tools Run this tool

bamtools stats description

Bamtools_stats prints general alignment statistics from the BAM file. More specifically, it will print total number of reads; number of mapped reads and how many of those are mapped to forward and reverse strand; how many reads have failed QC or are duplicate; how many pair-end reads are mapped and how many are singletons

Parent program: bamtools

BAMTools is a toolkit for managing genome alignment data in BAM and SAM formatted files. It is consists of set of tools for conversion, filtration, sorting, merging, and splitting files, or printing some basic and statistical information. BamTools can also generate BAI or BTI index files for BAM file. This suite shows some overlaps of manipulation modules with SAMtools toolkit but supports features that extend the abilities in genome alignment data analysis.