I have a very small doubt.
I am trying to generate a tab separated txt from my vcf file.I would like to assign the dbsnp match status ( showing novelity ) .I am not able to get this status .I have used snpeff to annotate vcf made from gatk Haplotypecaller .When I am selecting fields I am not able to assign the novelity status.Please help me in this regard.
These are the headers which I would like to see as output.
Chromosome Start End Reference Variant Allele Variant Type Sample Count Expt. Allele Frequency dbSNP Match Category dbSNP Id Strand Gene Gene Symbol Transcript Consequence Exon Number Position in cDNA Position in Protein Amino Acid Change SNP Call Total Reads Supporting Reads % Variant Reads % Zygosity Score .
Thanks in advance.