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I am following the GATK best practices workflow on Linux. I am using chr21.fa as reference from NCBI and .vcf files are taken from resource bundle and dbsnp.vcf is from NCBI.
I am working on the VariantRecalibrator step. It gives me NullPointerException. I am attaching the console error that I have got which contains the command also and raw_variants.vcf which is generated in previous step by HaplotypeCaller tool in txt format.
Please let me know what can be the issue.