I have been working with RealignerTargetCreator and in its pages, RealignerTargetCreator. It states that it takes multiple inputs as Bam. But its not taking it. when I checked Galaxy.it stated that GenomeAnalysisTK: RealignerTargetCreator accepts an aligned BAM input file.
I want to give all my Bam files for indel realigner intervals.
Here's the command that I am using; java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I input.bam -known indels.vcf -o forIndelRealigner.intervals
Your help is appreciated. Qurat