SeattleSeq Annotation 134
  

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 (limited):
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
gene locations to use:
NCBI full genes (NM, XM)
CCDS 2011 (coding regions only)
NCBI and CCDS 2011


or

Input Annotation File for Table Display

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

SeattleSeq Annotation 134 was most recently updated June 19, 2012. The current version is 7.05. The most recent site, based on dbSNP build 137, is at http://snp.gs.washington.edu/SeattleSeqAnnotation137.
May 17, 2012 -- new columns: KEGG Pathways, CpG Islands, TFBS, NHLBI ESP Allele Counts ... more
March 25, 2012 -- SNVs and indels in same VCF file, PolyPhen scores, GWAS hits
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