I'm attempting to annotate my M. tuberculosis variant VCF files using SnpEff. The genome build I used for the variant calling was gi|559794742|gb|CP003248.2| and the error i get when running the code below is: EFF=(MODIFIER||||||||||1|ERROR_CHROMOSOME_NOT_FOUND). I attempted to change the name of the chromosome to match that of the genome build (H37RV) used by SnpEff but it did not work. here is the genome link from SnpEff.config ftp://ftp.sanger.ac.uk/pub/pathogens/Mycobacterium/tuberculosis.
I too attempted to change this to the link the the genome i used which returned the same error.
java -jar snpEff.jar -i vcf -o vcf m_tuberculosis ./test1.vcf