Tool:NOVEL and Known Status in snp vcf file using snpeff annotation
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Entering edit mode
7.4 years ago
adinani149 • 0

Hi

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

snpeff snpsift novel-snp • 2.0k views
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