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BaseRecalibrator Unknown index type
I am trying to run BaseRecalibrator on my realigned files using GATK v3.5-0 and the following command
java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I realign.bam -knownSites known_snps.vcf -o data.table
but I am getting this error message "ERROR MESSAGE: Unknown index type. magic number: 0x0; type 0".
Any idea what could be wrong?
Thank you very much for your help,