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 (
an error will be thrown.
This can be fixed by using
samtools addreplacerg or
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.
For documentation and manuals visit our github.io page.
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.