SeattleSeq Annotation 147
Sponsored by
SeattleSNPs
and
SeattleSeq
About SeattleSeq Annotation
How to Use
Build Notes
Download Example Input Files
SeattleSeq Ann. 138 (hg19)
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Input Variation List File for Annotation
use reference NCBI 38/hg38
annotations for the NCBI gene model will be returned
enter e-mail address:
input file format:
(SNVs only unless otherwise indicated)
VCF SNVs and Indels
(SNVs and/or indels)
specify output file format:
SeattleSeq (tabular) file format
VCF file format
Maq
GFF3
specify attribute tags:
reference tag
genotype tag
CASAVA
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 Submitted
Genotype in dbSNP
dbSNP Individual ID:
Find an Individual ID
Alleles in dbSNP
Conservation Score GERP
CADD C Score
non-commercial applications only
Chimp Allele
Genes
HapMap Frequencies:
minor
reference
Has Genotypes
dbSNP Validation
Repeats
Protein Accession
cDNA Position
PolyPhen:
score HumDiv Model
class HumDiv Model
score HumVar Model
class HumVar Model
Clinical Association
Distance To Nearest Splice Site
microRNAs
Grantham Score
KEGG Pathways
CpG Islands
NHLBI ESP Allele Counts
split ESP Afr/Eur
ExAC Allele Counts
split ExAC Afr/Eur/Asn
Protein-Protein Interactions
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):
hg38 genomic location:
first allele (A, C, G, T):
second allele (A, C, G, T):
or
Input One Indel
(
VCF convention
)
chromosome (1-22, X, Y):
hg38 genomic location:
reference allele(s):
alternate allele(s):
SeattleSeq Annotation was most recently updated July 18, 2016. The current version is 12.01.
June 27, 2016 -- The dbSNP build is now 147. Variations mapped to hg38 are again required. ...
more
other recent -- Exome Aggregation Consortium allele counts have been added.
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