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Fig. 2 | Genome Medicine

Fig. 2

From: Cpipe: a shared variant detection pipeline designed for diagnostic settings

Fig. 2

Simplified Cpipe analysis steps. Cpipe consists of a number of steps. The core of these are based on the best practice guidelines published by the Broad Institute, consisting of alignment using BWA mem, duplicate removal using Picard MarkDuplicates, local realignment and base quality score recalibration using GATK, and variant calling using GATK HaplotypeCaller. To support clinical requirements, many steps are added including quality control steps (BEDTools coverage and QC summary), additional annotation (Annovar and the Variant Effect Predictor, VEP) and enhanced reports (Annotated variants, Provenance PDF, QC Excel report and Gap Analysis)

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