Hi I have DBSNP VCf file for my genome i used GATK for variant calling with option -d dbsnp.vcf No RS id were reported in my out.vcf . That means all my SNP in out.vcf is novel !?
Then i edited my dbsnp.vcf chromosome name same like my ref.fasta and bam file rerun GATK using this edited dbsnp.vcf. It gave me error saying "The provided VCF file is malformed at approximately line number 15: 0 is an invalid filter name in vcf4"
Will it be possible not to get any reported snps from dbsnp.vcf in my out.vcf ? Also what the above error means?