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4
votes
1
answer
156
views
1
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snpEff: wrong HGVS output?
hgvs snpeff written 12 days ago by Marvin • 120 • updated 4 days ago by WouterDeCoster ♦ 32k
0
votes
0
answers
106
views
0
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How to fetch GFF information for genome downloaded from ENA?
genome annotation snpeff snp oryza written 20 days ago by athulmenonk • 0 • updated 20 days ago by WouterDeCoster ♦ 32k
0
votes
2
answers
191
views
2
answers
Running vcf2maf on snpeff-annotated vcfs
snpeff vcf2maf written 9 weeks ago by becky3.a • 0
1
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0
answers
116
views
0
answers
Identify or update refseq transcript version on snpeff
ngs snpeff refseq variant-annotation written 6 weeks ago by Nandini • 670
6
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2
answers
193
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2
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how to extract gene name for LOF (loss of function) variants
snpeff lof variants written 6 weeks ago by reza • 190 • updated 6 weeks ago by Pierre Lindenbaum ♦ 112k
1
vote
0
answers
121
views
0
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build databses for genome using snpEff
annotation snpeff snp written 7 weeks ago by StudentBio • 0 • updated 7 weeks ago by finswimmer ♦ 5.5k
4
votes
1
answer
573
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5 follow
1
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more than one annotation at a locus in SnpEff output?
snpeff written 19 months ago by sun.nation • 120 • updated 8 weeks ago by jilguero888 • 10
1
vote
3
answers
1.9k
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3
answers
Issue converting VCF to MAF using snpEff annotations
maf vcf snpeff vcf2maf written 3.7 years ago by Marina Manrique • 1.3k • updated 8 weeks ago by sutturka • 120
2
votes
1
answer
154
views
1
answer
SNP difference between isolates
mycobacterium tuberculosis snpeff snp written 9 weeks ago by sanjay.bpkihs • 0 • updated 9 weeks ago by Medhat ♦ 7.7k
1
vote
1
answer
157
views
1
answer
How to Get only one annotation with the SnpEff annotation?
annotation variation snpeff snp written 10 weeks ago by mhmtgenc85 • 30 • updated 10 weeks ago by Pierre Lindenbaum ♦ 112k
2
votes
1
answer
106
views
1
answer
Error building snpEff database "Transcript 'hypothetical_protein' already exists"
database snpeff build written 10 weeks ago by Lina F • 150 • updated 10 weeks ago by Pierre Lindenbaum ♦ 112k
2
votes
0
answers
323
views
0
answers
Annotation with snpEFF
vcf annotation extractfields snpeff written 3 months ago by Nandini • 670 • updated 11 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
229
views
0
answers
SNPEff not showing SNP
annotation forum snpeff variant snp written 5 months ago by sanjay.bpkihs • 0 • updated 3 months ago by cpad0112 • 9.0k
0
votes
0
answers
185
views
0
answers
I need help to create 2 SNPEFF databases (v1.01/v2.01) of Pinus taeda
snpeff written 3 months ago by nie shuai • 0 • updated 3 months ago by Biostar ♦♦ 20
5
votes
3
answers
693
views
3
answers
number of functions is more than namber of variants in snpEff's output
next-gen snpeff snp written 18 months ago by reza • 190 • updated 4 months ago by finswimmer ♦ 5.5k
2
votes
5
answers
3.7k
views
5
answers
snpEFF chr not found error bacterial genome
annotation snpeff snp written 3.8 years ago by SemiQuant • 30 • updated 5 months ago by sanjay.bpkihs • 0
0
votes
1
answer
220
views
1
answer
Are there any working GNU parallel or similar Shell code examples on how to run Pilon, Prokka, VT and Snpeff tools on a batch of input files?
shell parallel snpeff gnu prokka written 5 months ago by england_bioinformatics_team • 10 • updated 5 months ago by jrj.healey ♦ 6.8k
1
vote
0
answers
320
views
0
answers
How to run SNPEff jar for a batch of VCF files using GNU parallel tool?
software variant calling snpeff gnu parallel bash written 7 months ago by oxfordsoccer • 10
0
votes
0
answers
503
views
0
answers
SnpSift doesn't show any VariantType for filtering
snpsift snpeff filtering mutations written 9 months ago by Bioinfo • 240 • updated 8 months ago by Biostar ♦♦ 20
0
votes
1
answer
788
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1
answer
Mutation analysis on RNAseq
next-gen snpeff mutation rna-seq snp written 24 months ago by Ron • 810 • updated 9 months ago by QVINTVS_FABIVS_MAXIMVS • 2.1k
3
votes
0
answers
534
views
0
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Annotation of VCF file
vcf snpeff mutation written 9 months ago by Bioinfo • 240 • updated 9 months ago by WouterDeCoster ♦ 32k
4
votes
2
answers
422
views
2
answers
Has anyone tried to run SNPEff, Bedtools or Prokka with GNU parallel or a similar batch engine?
bedtools parallel snpeff gnu prokka written 10 months ago by bioinformatics_bel • 20 • updated 10 months ago by WouterDeCoster ♦ 32k
1
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0
answers
569
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0
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SnpEff html and .vcf file result are not matching
vcf snpeff tool snp written 13 months ago by misbahabas • 60 • updated 11 months ago by Biostar ♦♦ 20
4
votes
1
answer
685
views
1
answer
[solved] SnpEff reports intron variants in exons ?
annotation snpeff exome-seq snp written 11 months ago by badredda • 50 • updated 11 months ago by cpad0112 • 9.0k
0
votes
0
answers
405
views
0
answers
how build database for single gene in snfeff
vcf alignment snpeff tool snp written 13 months ago by misbahabas • 60
0
votes
0
answers
474
views
0
answers
Show warnings and errors in snpeff summary
vcf snpeff tool snp written 13 months ago by misbahabas • 60
2
votes
1
answer
542
views
1
answer
Scoring whether genes are functional or not based on SIFT and SNPEff results
sift snpeff annotation written 14 months ago by jsgounot • 130 • updated 14 months ago by Emily_Ensembl ♦ 15k
0
votes
0
answers
488
views
0
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How to get more information about variants in intergenic regions?
annotation ngs snpeff variants written 14 months ago by ciemanek • 100
0
votes
1
answer
1.5k
views
1
answer
Error while building new database for SnpEff
database snpeff snp sequencing written 2.2 years ago by mjones1337 • 0 • updated 14 months ago by Santosh Anand • 3.9k
4
votes
1
answer
701
views
1
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Is SNPeff still the standard for variant effect prediction?
exome annotation snpeff variant written 14 months ago by Lauren • 20 • updated 14 months ago by Samuel Brady • 240
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