SeattleSeq Annotation 154
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
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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
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
Alleles in dbSNP
Conservation Score GERP
CADD C Score
non-commercial applications only
Chimp Allele
Genes
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 May 9, 2022. The current version is 16.01.
September 30, 2020 -- The dbSNP build is now 154. Variations mapped to hg38 are again required. ...
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National Heart, Lung, and Blood Institute
