Tool:NOVEL and Known Status in snp vcf file using snpeff annotation
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6.5 years ago
adinani149 • 0

Hii ,

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.

 

novel snp snpeff snpsift Tool • 1.8k views
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