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Summary statistics of VCF annotated files (snpEff)
vcf annotation snpeff statistics written 3 days ago by bwczech • 0
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80
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"count"in the snpEFF html output
snpeff written 10 days ago by lifang5389 • 0
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161
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snpEff assigned all variants as modifier intergenic
vcf ngs snpeff written 19 days ago by bwczech • 0
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1
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238
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1
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snpEff: wrong HGVS output?
hgvs snpeff written 9 weeks ago by Marvin • 120 • updated 7 weeks ago by WouterDeCoster ♦ 34k
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167
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How to fetch GFF information for genome downloaded from ENA?
genome annotation snpeff snp oryza written 10 weeks ago by athulmenonk • 0 • updated 10 weeks ago by WouterDeCoster ♦ 34k
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2
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259
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Running vcf2maf on snpeff-annotated vcfs
snpeff vcf2maf written 4 months ago by becky3.a • 0
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167
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Identify or update refseq transcript version on snpeff
ngs snpeff refseq variant-annotation written 3 months ago by Nandini • 700
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262
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how to extract gene name for LOF (loss of function) variants
snpeff lof variants written 3 months ago by reza • 190 • updated 3 months ago by Pierre Lindenbaum ♦ 114k
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build databses for genome using snpEff
annotation snpeff snp written 3 months ago by StudentBio • 0 • updated 3 months ago by finswimmer ♦ 6.8k
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more than one annotation at a locus in SnpEff output?
snpeff written 21 months ago by sun.nation • 120 • updated 3 months ago by jilguero888 • 10
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Issue converting VCF to MAF using snpEff annotations
maf vcf snpeff vcf2maf written 3.8 years ago by Marina Manrique • 1.3k • updated 3 months ago by sutturka • 120
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1
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181
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1
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SNP difference between isolates
mycobacterium tuberculosis snpeff snp written 3 months ago by sanjay.bpkihs • 0 • updated 3 months ago by Medhat ♦ 8.0k
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1
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1
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How to Get only one annotation with the SnpEff annotation?
annotation variation snpeff snp written 4 months ago by mhmtgenc85 • 30 • updated 4 months ago by Pierre Lindenbaum ♦ 114k
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1
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1
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Error building snpEff database "Transcript 'hypothetical_protein' already exists"
database snpeff build written 4 months ago by Lina F • 150 • updated 4 months ago by Pierre Lindenbaum ♦ 114k
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480
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Annotation with snpEFF
vcf annotation extractfields snpeff written 4 months ago by Nandini • 700 • updated 4 months ago by Biostar ♦♦ 20
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257
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SNPEff not showing SNP
annotation forum snpeff variant snp written 6 months ago by sanjay.bpkihs • 0 • updated 4 months ago by cpad0112 • 9.9k
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242
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I need help to create 2 SNPEFF databases (v1.01/v2.01) of Pinus taeda
snpeff written 5 months ago by nie shuai • 0 • updated 5 months ago by Biostar ♦♦ 20
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3
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3
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number of functions is more than namber of variants in snpEff's output
next-gen snpeff snp written 20 months ago by reza • 190 • updated 5 months ago by finswimmer ♦ 6.8k
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5
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5
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snpEFF chr not found error bacterial genome
annotation snpeff snp written 3.9 years ago by SemiQuant • 50 • updated 6 months ago by sanjay.bpkihs • 0
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262
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1
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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 6 months ago by england_bioinformatics_team • 10 • updated 6 months ago by jrj.healey ♦ 8.5k
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How to run SNPEff jar for a batch of VCF files using GNU parallel tool?
software variant calling snpeff gnu parallel bash written 9 months ago by oxfordsoccer • 10
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555
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SnpSift doesn't show any VariantType for filtering
snpsift snpeff filtering mutations written 11 months ago by Bioinfo • 270 • updated 10 months ago by Biostar ♦♦ 20
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1
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1
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Mutation analysis on RNAseq
next-gen snpeff mutation rna-seq snp written 2.1 years ago by Ron • 820 • updated 11 months ago by QVINTVS_FABIVS_MAXIMVS • 2.1k
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593
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Annotation of VCF file
vcf snpeff mutation written 11 months ago by Bioinfo • 270 • updated 11 months ago by WouterDeCoster ♦ 34k
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2
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2
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Has anyone tried to run SNPEff, Bedtools or Prokka with GNU parallel or a similar batch engine?
bedtools parallel snpeff gnu prokka written 12 months ago by bioinformatics_bel • 20 • updated 12 months ago by WouterDeCoster ♦ 34k
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SnpEff html and .vcf file result are not matching
vcf snpeff tool snp written 15 months ago by misbahabas • 60 • updated 13 months ago by Biostar ♦♦ 20
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1
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[solved] SnpEff reports intron variants in exons ?
annotation snpeff exome-seq snp written 13 months ago by badredda • 50 • updated 13 months ago by cpad0112 • 9.9k
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443
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how build database for single gene in snfeff
vcf alignment snpeff tool snp written 15 months ago by misbahabas • 60
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503
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Show warnings and errors in snpeff summary
vcf snpeff tool snp written 15 months ago by misbahabas • 60
2
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1
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575
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1
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Scoring whether genes are functional or not based on SIFT and SNPEff results
sift snpeff annotation written 15 months ago by jsgounot • 130 • updated 15 months ago by Emily_Ensembl ♦ 16k
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