NGS Mapping Dissection
This chapter gives a dissection of the NGS Mapping step (ngs_mapping
) for CUBI pipeline developers.
The NGS mapping step is an example for a pipeline step that works on the raw FASTQ NGS read files.
This chapter assumes that you have read Somatic Variant Calling Dissection before.
The minority of pipeline steps will work directly with the raw read data. Most steps work on the results of the NGS read mapping step or even further downstream.
Note
Before reading this chapter, you should
have knowledge from the user’s perspective of CUBI pipeline (start a Usage)
have read chapter Developer’s Introduction
have read chapter Somatic Variant Calling Dissection.
After reading this chapter, you should
know how to work with raw FASTQ file input
know how to use the using the
LinkInStep
This is still TODO, just look at the code for now ;)