Tagged with #indel-realignment
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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.

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