This tool extracts reads from a BAM file based on alignment intervals. E.g if one is interested in a specific location this tool extracts the full reads from the location. The tool is also very useful to create test data sets.


For documentation and manuals visit our github.io page.


ExtractAlignedFastq 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.


For any question related to ExtractAlignedFastq, please use the github issue tracker or contact the SASC team directly at: [email protected].