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4
votes
1
answer
77
views
1
answer
IMPACT rating in VEP and compatibility with which tools?
impact rating vep written 12 days ago by Shicheng Guo • 7.5k • updated 12 days ago by Ben_Ensembl • 1.0k
0
votes
0
answers
172
views
0
answers
patients hg19 VEP Fasta and CACHE GRCh37
ensembl grch37 vep hg19 written 9 weeks ago by cocchi.e89 • 20 • updated 16 days ago by Biostar ♦♦ 20
1
vote
0
answers
69
views
0
answers
unauthorized: authentication required error in ensembl-vep installation
vep vep (variant effect predictor) written 19 days ago by Shicheng Guo • 7.5k
4
votes
1
answer
126
views
1
answer
How does VEP decide on canonical transcripts and is there a list?
assembly vep written 27 days ago by hagen.klett • 0
8
votes
4
answers
1.3k
views
4
answers
Protein coding transcripts with vep
annotation vep variants written 3.3 years ago by onemoreuser • 10 • updated 6 weeks ago by abio • 0
3
votes
1
answer
162
views
1
answer
Ensembl variant effect predictor fails if REF or ALT allele has a length around 0.5 million
vcf ensembl vep vcf annotation written 6 weeks ago by mo.imranshah • 10
3
votes
1
answer
167
views
1
answer
ensembl VEP variant not annotated
ensembl variants vep annotation written 7 weeks ago by cocchi.e89 • 20
3
votes
1
answer
194
views
1
answer
The content of variation (VEP) file from Ensembl
ensembl vep human written 8 weeks ago by seta • 1.2k • updated 8 weeks ago by Emily_Ensembl ♦ 18k
2
votes
1
answer
168
views
1
answer
Calculate the allele frequency of specific sub-population using VEP
allele frequency vep written 8 weeks ago by Abdul Rafay Khan • 1.0k • updated 8 weeks ago by Emily_Ensembl ♦ 18k
1
vote
1
answer
169
views
1
answer
VEP dbNSFP plugin GRCh37
ensembl anotation dbnsfp vep plugin written 9 weeks ago by cocchi.e89 • 20 • updated 9 weeks ago by Emily_Ensembl ♦ 18k
3
votes
1
answer
188
views
1
answer
VEP FASTA "toplevel" vs "primary_assembly"
fasta ensembl vep written 9 weeks ago by cocchi.e89 • 20
0
votes
0
answers
216
views
0
answers
VEP annotation of Manta BND
annnotation vep written 10 weeks ago by lindak • 0 • updated 10 weeks ago by Emily_Ensembl ♦ 18k
7
votes
2
answers
505
views
5 follow
2
answers
VEP output and stop gain mutation
ensembl vep stop gain written 7 months ago by seta • 1.2k • updated 3 months ago by zx8754 ♦ 7.5k
0
votes
0
answers
455
views
0
answers
Bio-DB-HTS installation and ensembl-vep
bio-db-hts vep ensembl written 3 months ago by felipead66 • 30 • updated 3 months ago by Emily_Ensembl ♦ 18k
3
votes
0
answers
218
views
0
answers
Updated Alignment of current refseq transcripts against hg19
genome refseq alignment vep hg19 written 4 months ago by cruckert • 10
14
votes
2
answers
408
views
7 follow
2
answers
bcftools query missense_variant SNPs from gnomad VCF files
bcftools vep written 4 months ago by Shicheng Guo • 7.5k • updated 4 months ago by Emily_Ensembl ♦ 18k
1
vote
1
answer
250
views
1
answer
Conserv CSQ and output plugin
ensembl vep csq written 5 months ago by robertclerc • 0 • updated 5 months ago by Emily_Ensembl ♦ 18k
1
vote
1
answer
658
views
1
answer
Using VEP to get gnomAD frequencies
annotation frequency vep gnomad allele frequency written 5 months ago by brett.spurrier • 20 • updated 5 months ago by Emily_Ensembl ♦ 18k
2
votes
1
answer
259
views
1
answer
Annovar and VEP overlapp
annovar vep written 6 months ago by BAGeno • 130 • updated 6 months ago by Kevin Blighe ♦ 44k
0
votes
1
answer
357
views
1
answer
Vep loftool threshold
loftool vep written 6 months ago by BAGeno • 130 • updated 6 months ago by Emily_Ensembl ♦ 18k
7
votes
1
answer
445
views
1
answer
VEP outputs more rs ids than input, why?
ensembl vep snp written 7 months ago by Uday Rangaswamy • 120
9
votes
1
answer
317
views
6 follow
1
answer
Assembly used in Variant Effect Predictor
ensembl vep snp written 7 months ago by Uday Rangaswamy • 120 • updated 7 months ago by Emily_Ensembl ♦ 18k
4
votes
1
answer
318
views
1
answer
Error when running Ensembl VEP: "bigWigToWig does not seem to be in your path"
ensembl ngs vep snp bigwig written 8 months ago by claudiadast • 0 • updated 7 months ago by Biostar ♦♦ 20
10
votes
2
answers
474
views
2
answers
Querying VEP using REST API
rest ensembl vep python R written 8 months ago by Arko • 20 • updated 8 months ago by Emily_Ensembl ♦ 18k
5
votes
1
answer
727
views
6 follow
1
answer
VEP- What is the best idea to start analyzing?
ensembl vep snp written 8 months ago by mostafarafiepour • 60 • updated 8 months ago by sadri.amirhossein • 10
21
votes
1
answer
1.2k
views
6 follow
1
answer
how to generate CNV plot from VEP results
cnv plot vep copy number alteration written 8 months ago by nazaninhoseinkhan • 360 • updated 8 months ago by Kevin Blighe ♦ 44k
15
votes
3
answers
552
views
7 follow
3
answers
Alternative to VEP.
vep snp written 9 months ago by joselu • 80 • updated 9 months ago by Emily_Ensembl ♦ 18k
1
vote
1
answer
1.1k
views
1
answer
Ensembl VEP cannot parse HGVS notation.
hgvs ensembl vep ref_seq parsing written 3.1 years ago by gmora • 20 • updated 9 months ago by zx8754 ♦ 7.5k
6
votes
1
answer
1.5k
views
8 follow
1
answer
Installing ensembl 86 VEP and vcf2maf and getting SNP MAFs
maf 1000genomes vep vcf2maf ensembl written 2.0 years ago by eurioste • 20 • updated 9 months ago by zx8754 ♦ 7.5k
1
vote
0
answers
414
views
0
answers
Keep Format and Individual fields after annotating VCF with VEP
vcf annotation vep csq info written 9 months ago by MasMarius • 10
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