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(howto) Perform local realignment around indels

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,816Administrator, GATK Developer admin
edited July 2013 in Tutorials

Objective

Perform local realignment around indels to correct mapping-related artifacts.

Prerequisites

  • TBD

Steps

  1. Create a target list of intervals to be realigned
  2. Perform realignment of the target intervals



1. Create a target list of intervals to be realigned

Action

Run the following GATK command:

java -jar GenomeAnalysisTK.jar \ 
-T RealignerTargetCreator \
-R reference.fa \
-I dedup_reads.bam \
-L 20 \
-known gold_indels.vcf \
-o target_intervals.list

Expected Result

This creates a file called target_intervals.list containing the list of intervals that the program identified as needing realignment within our target, chromosome 20.

The list of known indel sites (gold_indels.vcf) are used as targets for realignment. Only use it if there is such a list for your organism.




2. Perform realignment of the target intervals

Action

Run the following GATK command:

java -jar GenomeAnalysisTK.jar \ 
-T IndelRealigner \
-R reference.fa \
-I dedup_reads.bam \
-targetIntervals target_intervals.list \
-known gold_indels.vcf \
-o realigned_reads.bam

Expected Result

This creates a file called realigned_reads.bam containing all the original reads, but with better local alignments in the regions that were realigned.

Note that here, we didn’t include the -L 20 argument. It's not necessary since the program will only run on the target intervals we are providing.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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