SeattleSeq Annotation 131
  

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

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input file format:
(SNPs only unless otherwise indicated)
Maq
GFF
CASAVA
VCF (SNPs only)
custom
one genotype per line
GATK bed (indels only)
VCF (indels only)
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 Prediction (limited locations)
Clinical Association
Distance To Nearest Splice Site
microRNAs
Grantham Score
gene locations to use:
NCBI full genes (NM, XM)
CCDS 2010 (coding regions only)
NCBI and CCDS 2010


or

Input Annotation File for Table Display

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

SeattleSeq Annotation was most recently updated October 7, 2013. The current version is 6.22. The most recent site, based on dbSNP build 137, is at http://snp.gs.washington.edu/SeattleSeqAnnotation137.
March 11, 2011 -- cDNA position added ... more
February 16, 2011 -- Grantham scores, simple indels in VCF format.
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