SeattleSeq Annotation
Sponsored by
SeattleSNPs
and
SeattleSeq
About SeattleSeq Annotation
How to Use
Build Notes
SeattleSeq Annot. 131
Download Example Input Files
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Input Variation List File for Annotation (NCBI 36 / hg18)
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input file format:
(SNPs only unless otherwise indicated)
Maq
GFF
CASAVA
VCF
specify output file format:
original output file format
VCF output file format
custom
specify column numbers (first is 1):
chromosome
location
reference allele (0 if not present)
first allele
second allele (can be same as first allele column)
one genotype per line
output is
one genotype per line format
GATK bed
(indels only)
add more annotation:
Alleles Called by Maq
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
PolyPhen Prediction (limited locations, CCDS only)
Clinical Association
Distance To Nearest Splice Site
gene locations to use:
NCBI full genes (NM, XM)
CCDS 2007 (coding regions only)
CCDS 2008 (coding regions only)
NCBI and CCDS 2007
NCBI and CCDS 2008
or
Input Annotation File for Table Display
SeattleSeq Annotation was most recently updated April 20, 2011. The current version is 5.07.
September 27, 2010 -- Limited annotation is available for indels (GATK bed format). ...
more
December 21, 2009 -- Presence of a SNP in 1000 Genomes added.
National Heart, Lung, and Blood Institute
National Human Genome Research Institute
National Heart, Lung, and Blood Institute
National Human Genome Research Institute