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(BP1.2) Local Realignment around Indels

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,904Administrator, GATK Developer admin

This article is part of the workflow documentation describing the Best Practices for Variant Discovery in DNAseq data. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow.

The algorithms that are used in the initial mapping step tend to produce various types of artifacts. For example, reads that align on the edges of indels often get mapped with mismatching bases that might look like evidence for SNPs, but are actually mapping artifacts. The realignment process identifies the most consistent placement of the reads relative to the indel in order to clean up these artifacts. It occurs in two steps: first the program identifies intervals that need to be realigned, then in the second step it determines the optimal consensus sequence and performs the actual realignment of reads.

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Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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