java -jar GenomeAnalysisTK.jar -R exampleFASTA.fasta -I exampleBAM.bam -T RealignerTargetCreator -o exampleTarget.intervals
I used the example files, and I got no error report, but in the output, there is no data, that is to say. The exampleTarget.intervals is empty.
Why is this happening?
And when I add --known dbsnp_135.hg19.vcf( that is in the bundle), it will get an error