RealignerTargetCreator gets a empty file, why?
Posted in Ask the GATK team | Last updated on 2012-11-01 19:16:53

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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

ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but different lengths:
ERROR contig known = chr1 / 249250621
ERROR contig reference = chr1 / 100000.

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