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8
votes
1
answer
73
views
1
answer
What is the VEP Impact column?
consequence sequencing vep variant ensembl written 8 days ago by nub6 • 20 • updated 6 days ago by werewxcvv • 0
2
votes
1
answer
75
views
1
answer
How to determine significance of a variant?
next-gen vep written 10 days ago by nub6 • 20 • updated 10 days ago by Hamid Ghaedi • 580
0
votes
0
answers
141
views
0
answers
VEP - gnomAD v3 (hg38) annotation AF
vep hg38 gnomad annotation written 6 weeks ago by cocchi.e89 • 110 • updated 22 days ago by Biostar ♦♦ 20
5
votes
1
answer
137
views
1
answer
Finding unique variants by sample ID in a multisample vcf
vcf bcftools vep snp written 5 weeks ago by tacrolimus • 50 • updated 5 weeks ago by brunobsouzaa • 370
2
votes
0
answers
107
views
0
answers
Ensembl FTP Mirror in USA? Slow Downloads
ensembl vep written 6 weeks ago by QVINTVS_FABIVS_MAXIMVS • 2.4k
2
votes
1
answer
130
views
1
answer
Use VEP (ensembl) with specific database e.g. dbSNP 144
ensembl vep snp mutation annotation written 8 weeks ago by romain.lannes • 80 • updated 8 weeks ago by Ben_Ensembl • 1.6k
0
votes
0
answers
118
views
0
answers
Counting allele counts/frequencies from a vcf file with both cases and controls
bcftools allele count vep written 9 weeks ago by tacrolimus • 50
0
votes
1
answer
323
views
1
answer
an efficient way to annotate mutations from vcf files using multiple annotation files
lovd ensembl clinvar vep cadd written 10 months ago by lait • 150 • updated 9 weeks ago by Biostar ♦♦ 20
4
votes
2
answers
237
views
2
answers
How can I use my own genome file on Variant Effect Predictor (VEP)
ensembl vep variant effect predictor written 11 weeks ago by caro-ca • 20 • updated 10 weeks ago by Ben_Ensembl • 1.6k
1
vote
1
answer
169
views
1
answer
Geneid between regions of chromosome
ensembl biomart vep geneid written 10 weeks ago by devarora • 240 • updated 10 weeks ago by Ben_Ensembl • 1.6k
0
votes
0
answers
162
views
0
answers
No results from VEP. What am I doing wrong?
software error vep snp written 3 months ago by rsnewbie • 0 • updated 3 months ago by zx8754 ♦ 9.7k
3
votes
1
answer
118
views
1
answer
VEP output and protein change
vcf vep written 3 months ago by MAPK • 1.6k • updated 3 months ago by RamRS ♦ 30k
2
votes
1
answer
120
views
1
answer
How to combining VEP and VCF in one file
vcf vep written 3 months ago by MAPK • 1.6k • updated 3 months ago by Pierre Lindenbaum ♦ 131k
0
votes
2
answers
165
views
2
answers
VEP cache trancript versions
annotation ngs dna-seq vep sequencing written 4 months ago by Chadi Saad • 80 • updated 3 months ago by Michal @Ensembl • 70
1
vote
0
answers
191
views
0
answers
Annotate hs37d5 genome calls using VEP
annotation 1kgenomes vep hs37d5 written 4 months ago by igor • 0
0
votes
0
answers
199
views
0
answers
Why snpEff annotates same region with different "effects" and why some effects are given in combination? What is the criteria to filter this annotation?
exome vcf snpeff vep variantannotation written 4 months ago by svp • 240
2
votes
1
answer
173
views
1
answer
VEP is returning MOTIF_NAME values not recognised by Ensembl
ensembl vep snp written 4 months ago by jeni • 30 • updated 4 months ago by Michal @Ensembl • 70
0
votes
0
answers
192
views
0
answers
Error while running vcf2maf tool
variant-calling maf vep vcf2maf vcfs written 4 months ago by Jordan • 1.2k
1
vote
2
answers
217
views
2
answers
Conversion of Vep.vcf to MAF format?
maf genome vep snp cancer written 5 months ago by Thind amarinder • 90
0
votes
1
answer
226
views
1
answer
VEP and gnomAD AF inconsistencies
ensembl vep gnomad af dbnsfp written 5 months ago by cocchi.e89 • 110 • updated 5 months ago by Ben_Ensembl • 1.6k
2
votes
1
answer
199
views
1
answer
VEP 100 and GRCh37
fasta ensembl grch37 vep written 5 months ago by cocchi.e89 • 110 • updated 5 months ago by Ben_Ensembl • 1.6k
9
votes
1
answer
333
views
1
answer
Get clinVar info for SNP with VEP
vep snp written 5 months ago by Eugene A • 80 • updated 5 months ago by Kevin Blighe ♦ 66k
3
votes
1
answer
167
views
1
answer
VEP outputs the similar INFO CSQ data multiple times
vcf tsv vep ensembl annotation written 5 months ago by magnolia • 0 • updated 5 months ago by Pierre Lindenbaum ♦ 131k
0
votes
1
answer
183
views
1
answer
Deformed VCF header and VEP
vcf annotation vep written 6 months ago by plink_9857 • 50 • updated 6 months ago by Astrid_Ensembl • 330
0
votes
0
answers
364
views
0
answers
DBD::SQLite::db prepare failed: no such table: phylocsf_summary
vep phylocsf loftee written 8 months ago by nikitavlassenko • 50 • updated 6 months ago by Biostar ♦♦ 20
3
votes
1
answer
166
views
1
answer
using vep with custom genome
vep snp written 6 months ago by etay.rot • 10 • updated 6 months ago by Ben_Ensembl • 1.6k
6
votes
1
answer
427
views
1
answer
News: Ensembl reduced functionality: 10th March-16th April 2020
ensembl news vep service blat written 8 months ago by Ben_Ensembl • 1.6k
0
votes
1
answer
154
views
1
answer
VEP MutationAssessor output
vep mutationassessor variant human written 6 months ago by cocchi.e89 • 110 • updated 6 months ago by Ben_Ensembl • 1.6k
3
votes
1
answer
195
views
1
answer
VEP order most severe to least
variant consequence wgs vep largevcf written 7 months ago by shwethacm • 210 • updated 7 months ago by Ben_Ensembl • 1.6k
2
votes
1
answer
215
views
1
answer
Alternative allele in VEP output
vcf wgs vep written 7 months ago by A • 3.9k • updated 7 months ago by Ben_Ensembl • 1.6k
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