SeattleSeq Annotation 137
Sponsored by
SeattleSNPs
and
SeattleSeq
About SeattleSeq Annotation
How to Use
Build Notes
Download Example Input Files
SeattleSeq Annot. for hg18
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Input Variation List File for Annotation (NCBI 37 / hg19)
enter e-mail address:
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
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)
VCF
(indels only)
specify output file format:
SeattleSeq Annotation original allele columns
VCF-like allele columns
VCF SNVs and Indels
(both)
specify output file format:
SeattleSeq Annotation file format
VCF file format
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):
SeattleSeq Annotation was most recently updated June 13, 2013. The current version is 8.06.
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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