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Pindel Annotation

Description

Pindel Annotation is a somatic mutation annotation pipeline used in GDC whole exome sequencing (WXS) and targeted sequencing harmonization.

Overview

Pindel Annotation is a pipeline used for WXS and targeted sequencing somatic mutation annotation at the GDC. Somatic mutation annotation is performed by annotating raw VCFs, which produces annotated somatic mutation files.

Input

  • Raw VCF - WXS or Targeted Sequencing

Output

  • MAF (Data Type: Annotated Somatic Mutation)
  • VCF (Data Type: Annotated Somatic Mutation)

References

  1. Pindel Command Line Parameters at the GDC
  2. DNA Seq Processing at the GDC

Categories: Workflow Type