SeattleSeq Annotation 137
  

Input Variation List File for Annotation (NCBI 37 / hg19)

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input file format:
(SNVs only unless otherwise indicated)
Maq
GFF
CASAVA
VCF (SNVs only)
  specify output file format:
SeattleSeq Annotation file format
VCF file format
custom
one genotype per line
GATK bed (indels only)
VCF (indels only)
VCF SNVs and Indels (both)
add more annotation:
Alleles Submitted
Genotype in dbSNP
dbSNP Individual ID:
Find an Individual ID
Alleles in dbSNP
Conservation Score phastCons
Conservation Score GERP
Chimp Allele
Copy Number Variations
Genes
HapMap Frequencies:
minor
reference
Has Genotypes
dbSNP Validation
Repeats
Protein Sequence
cDNA Position
PolyPhen:
class
score
Clinical Association
Distance To Nearest Splice Site
microRNAs
Grantham Score
KEGG Pathways
CpG Islands
Transcription Factor Binding Sites (takes more time)
NHLBI ESP Allele Counts
split ESP Afr/Eur
Protein-Protein Interactions
gene locations to use:
NCBI full genes (NM, XM) -- the fastest choice
CCDS 2012 (coding regions only)
NCBI and CCDS 2012


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):
hg19 genomic location:
first allele (A, C, G, T):
second allele (A, C, G, T):

SeattleSeqAnnotation137 was most recently updated October 13, 2013. The current version is 8.08. The most recent site, based on dbSNP build 147, and hg38/NCBI 38, is at http://snp.gs.washington.edu/SeattleSeqAnnotation147.
November 14, 2012 -- The dbSNP build is now 137. Many updates, more PolyPhen-2 ... more
May 17, 2012 -- new columns: KEGG Pathways, CpG Islands, TFBS, NHLBI ESP Allele Counts
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