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Pindel

Description

Pindel is a somatic variant calling pipeline used in GDC whole genome sequencing (WGS), whole exome sequencing (WXS) and targeted sequencing harmonization.

Overview

Pindel is one of the pipelines used for WGS, WXS and targeted sequencing somatic variant calling at the GDC. Somatic variant calling is performed with Pindel using tumor and normal alignments and generates indel data.

Input

  • Tumor BAM - WGS, WXS or Targeted Sequencing
  • Normal BAM - WGS, WXS or Targeted Sequencing

Output

  • VCF (Data Type: Raw Simple Somatic Mutation)

References

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

Categories: Workflow Type