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Bamstats

Bamstats is a command line tool written in Go for computing mapping statistics from a BAM file.

Installation instructions

Use one of the following methods to install Bamstats.

Install a released version

The easiest way is to download a pre-compiled binary from Github releases. Here is an example for installing the latest released version on Linux 64bit:

export VERSION=0.3.5 OS=linux ARCH=x86_64 BIN=/usr/local/bin
wget -O - https://github.com/guigolab/bamstats/releases/download/v${VERSION}/bamstats-v${VERSION}-${OS}-${ARCH}.tar.gz | tar xz -C ${BIN} bamstats

Install the latest version with go

The following command will install the latest version from the master branch into $GOPATH:

go get github.com/guigolab/bamstats/cmd/bamstats

Provided statistics

Bamstats can currently compute the following mapping statistics:

• general
• genome coverage
• RNA-seq

General

The general mapping statistics include:

• Total number of reads
• Number of unmapped reads
• Number of mapped reads grouped by number of multimaps (NH tag in BAM file)
• Number of mappings
• Ratio of mappings vs mapped reads

If the data is paired-end, a section for read-pairs is also reported. In addition to the above metrics, the section contains a map of the insert size length and the corresponding support as number of reads.

Genome coverage

The genome coverage ststistics are computed for RNA-seq data and include counts for the following genomic regions:

• exon
• intron
• exonic_intronic
• intergenic
• others

The above metrics are computed for continuous and split mapped reads. An aggregated total is computed across elements and read types too.

The --uniq (or -u) command line flag allows reporting of genome coverage statistics for uniquely mapped reads too.

RNA-seq

The RNA-seq statistics follow IHEC reccomendations for RNA-seq data quality metrics. They include counts for the following regions:

• intergenic (different from coverage stats)
• ribosomal RNA (rRNA)

As long as other fractional metrics for the following read types:

• mapped
• intergenic
• rRNA
• duplicates

Output examples:

Some examples of the program output can be found in the data folder ot this GitHub repository:

• General Stats
• Genomic coverage stats
• Genomic coverage stats with uniquely mapped reads (Note that the coverageUniq stats are reported as an additional JSON object)
• RNA-seq stats

Please see here for a complete description of the output fields and how they are calculated.

License

This software is release under a BSD-style license. Please check the LICENSE file for more details.