Requested files for RealignerTargetCreator (GATK)

Having a .fa file with a specific region or a single chromosome we must create the .dict and the .fai file to use the RealignerTargetCreator from GATK.

To create the .dict file we use the CreateSequenceDictionary from Picard:

java -jar CreateSequenceDictionary.jar 
    R=GRCh37.73.dna.22.fa 
    O=GRCh37.73.dna.22.dict

This will create the file GRCh37.73.dna.22.dict.

The .fai file is created using samtools:

samtools faidx GRCh37.73.dna.22.fa

This command will create the file GRCh37.73.dna.22.fa.fai.

And, having the three files (.fa, .dict and .fa.fai) we are able to call the GATK:

java -Xmx4g -jar GenomeAnalysisTK.jar 
    -T RealignerTargetCreator 
    -I chr22.sort.marked.bam 
    -R GRCh37.73.dna.22.fa 
    -o chr22.bam.list
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