interval output in DiagnoseTargets
I've ran DiagnoseTargets with the following command:
java -jar GenomeAnalysisTK.jar -T DiagnoseTargets -R Final.HMP.fasta -o diag.output.vcf -I bam.list -L interval.list
But for some reason, my output is only one line per chromosome. there are two output files: diag.output.vcf, diag.output.vcf.idx.
How come there is no file for interval outputs?
My interval names look like this: lcl|NC_011004.1-5739, is there a problem with this naming? (I hope not..)
Thanks again for all your help!