SeattleSeq Annotation 141
  

Input Variation List File for Annotation

use reference NCBI 38/hg38
annotations for the NCBI gene model will be returned
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input file format:
(SNVs only unless otherwise indicated)
VCF SNVs and Indels (SNVs and/or indels)
  specify output file format:
SeattleSeq (tabular) file format
VCF file format
Maq
GFF3
CASAVA
custom
one genotype per line
GATK bed (indels only)
add more annotation:
Alleles Submitted
Genotype in dbSNP
dbSNP Individual ID:
Find an Individual ID
Alleles in dbSNP
Conservation Score GERP
CADD C Score non-commercial applications only
Chimp Allele
Genes
HapMap Frequencies:
minor
reference
Has Genotypes
dbSNP Validation
Repeats
Protein Accession
cDNA Position
PolyPhen:
class
score
Clinical Association
Distance To Nearest Splice Site
microRNAs
Grantham Score
KEGG Pathways
CpG Islands
NHLBI ESP Allele Counts
split ESP Afr/Eur
ExAC Allele Counts
split ExAC Afr/Eur/Asn
Protein-Protein Interactions


or

Input Annotation File for Table Display

does not yet support VCF-in-VCF-out or one-genotype-per-line


or

Input One SNV

chromosome (1-22, X, Y):
hg38 genomic location:
first allele (A, C, G, T):
second allele (A, C, G, T):

SeattleSeq Annotation was most recently updated April 12, 2015. The current version is 10.02.
April 12, 2015 -- Exome Aggregation Consortium allele counts have been added.
other recent -- The dbSNP build is now 141. Variations mapped to hg38 are required.
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