BaseSpace VariantStudio User Guide

Index

1

1000 Genomes

annotation source 67

in variants table 14

A

alelle frequency 14, 45

annotation

commands 26 custom 26

options 27

sources 66

transcript source 27

B

BaseSpace File Browser 6

BED file, importing 10

C

cancer analysis pipeline 22

canonical transcript 27

classification filter 47

classifications

adding, removing 35

applying to variants 31 database 31

database backup 36 database storage options 36

edit database 33

importing 37

in reports 60

in variants table 12

report fragments 31

ClinVar

annotation source 67

filter annotations with 43

in variants table 16

codon, intiatator 44

consequence 14

consequence filters 44

COSMIC

annotation source 67

filter annotations with 43

in variants table 15

cross sample subtraction filter 45

custom annotation 26

applying 29 creating 29

filters 47

in variants table 13

input file, genes 29 input file, variants 29

customer support 71

D

de novo mutation, filtering by 46

BaseSpace VariantStudio v2.2 Software User Guide

deletion, in-frame 44

documentation 71

dominant transmission, filtering by 46

E

Ensembl

annotation source 66

in variants table 14

Entrez Gene ID 16

EVS 45

F

family based filtering 46

favorite filters 55

filters

advanced 41

applying 7

classification 47

clear history 7 clearing 7

consequence 44

creating favorites 55

cross sample substraction 45

custom 47

family based 46

gene 43

general 41

history pane 7

history reporting 63

interface 6

population frequency 45

variants 43

filters pane 7, 40

frameshift 44

G

Gene ID 16

gene list

filtering 43

importing from 10

gene view 8

GeneReviews 17

genes table 16

genome VCF 5

GQX

in variants table 13

in VCF file 21

H

help, technical 71

HGNC

in variants table 14 transcript in variants table 14

HGVS 14

histogram, creating 63

69

70

I

import commands 10 import options 10

initiator codon 44

input file

default transcripts 28

insertion, in-frame 44

installation, side-by-side 3

M

missense 44

N

NCBI 67

NHLBI Exome Variant Server 68

no-call regions table 17

P

padding with import 10

pie chart, creating 63

PolyPhen 14, 44

population frequency 45

PubMed

in genes table 17

R

recessive transmission, filtering by 46

reporting

filter history 63

sample report 59, 62

templates 60

variants 63

reports 58

requirements

system 2

VCF input 4

S sample reports

creating 59, 62

creating a templates 60

SIFT 14, 44

somatic variant calls 22

splice 44

system requirements 2

T

table views, modifying 18

tables

genes 6, 16

no-call regions 6, 17

variants 6, 12

technical assistance 71

templates

example report 60 sample report 60

transcript source 27

transcripts

input file 27

input file, default transcripts 28

setting default 27

U

UCSC 68

V variants

add to current sample 10

annotating 26

importing 10

variants table 12

VCF files

fields in the variants table 21

gVCF 5

import options 10 importing 10

requirements 4

somatic VCF 22

VEP 66

W

workflow 2

X

X-linked variants, filtering by 46

Part # 15047059 Rev. A