BamStats

BamStats is a package that contains tools to generate stats from a BAM file, merge those stats for multiple samples, and validate the generated stats files.

Mode - Generate

Generate reports clipping stats, flag stats, insert size and mapping quality on a BAM file. It outputs a JSON file, but can optionally also output in TSV format.

The output of the JSON file is organized in a sample - library - readgroup tree structure. If readgroups in the BAM file are not annotated with sample (SM) and library (LB) tags an error will be thrown. This can be fixed by using samtools addreplacerg or picard AddOrReplaceReadGroups.

Mode - Merge

This module will merge bamstats files together and keep the sample/library/readgroup structure. Values for the same readgroups will be added. It will also validate the resulting file.

Mode - Validate

Validates a BamStats file. If aggregation values can not be regenerated the file is considered corrupt. This should only happen when the file has been manually edited.

Documentation

For documentation and manuals visit our github.io page.

About

BamStats is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.

Contact

For any question related to BamStats, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.