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Table of Contents
2.1 Primary Analysis - Sequence processing
After sequencing, reads are mapped to the human genome reference (GRCh37). Then, there are some filtering steps in which the number of reads decreases until variant calling. Here, we describe how this reduction occurs in each pipeline.
BIER's pipeline
In this pipeline, there are four stages where the number of reads decreases (mapping, filter by mapping quality, remove duplicates and intervals realignment). This table shows
CNAG's pipeline
