18/09/2019 GitHub - guigolab/bamstats: A command line tool to compute mapping statistics from a BAM file
guigolab / bamstats
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A command line tool to compute mapping statistics from a BAM file
223 commits 3 branches 7 releases 1 contributor BSD-3-Clause
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emi80 Bump version to 0.3.3 for release Latest commit a97df7c 14 days ago
annotation Fix wrong feature merging and interleaving with unsorted annotation - c… 14 days ago
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config Add missing config package 3 years ago
data Add check for int8 NH tag in general stats - fix #18 11 months ago
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scripts Add preprocessing scripts to repo last year
stats Add check for int8 NH tag in general stats - fix #18 11 months ago
utils Add method to [Link] to output JSON - close #16 last year
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[Link] [ci skip] Update installation instructions in readme to use latest re… 10 months ago
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[Link] Switch to Go Modules - close #22 15 days ago
[Link] Switch to Go Modules - close #22 15 days ago
process_test.go Add check for int8 NH tag in general stats - fix #18 11 months ago
[Link] Bump version to 0.3.3 for release 14 days ago
[Link]
Bamstats
build passing coverage 85%
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
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18/09/2019 GitHub - guigolab/bamstats: A command line tool to compute mapping statistics from a BAM file
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=0.3.2 OS=linux ARCH=amd64 BIN=/usr/local/bin
wget -O - [Link]
v${VERSION}-${OS}-${ARCH}.tar.bz2 | tar xj --strip-components 3 -C ${BIN}
Install the latest version with go
The following command will install the latest version from the master branch into $GOPATH :
go get [Link]/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
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18/09/2019 GitHub - guigolab/bamstats: A command line tool to compute mapping statistics from a BAM file
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
License
This software is release under a BSD-style license. Please check the LICENSE file for more details.
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