Showing : variantannotation • reset
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75
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
13 days ago Stevie Pederson • 0
0
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1
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140
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Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 6 weeks ago by 65k • written 6 weeks ago by ▴ 170
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155
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
3 months ago Vincent J. Carey, Jr. 6.7k
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5
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468
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 4 months ago by 65k • written 4 months ago by ▴ 30
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440
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
7 months ago Bogdan ▴ 670
2
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2
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1.5k
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Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by ★ 1.5k
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2
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536
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 11 months ago by ★ 4.0k • written 11 months ago by • 0
4
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8
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1.4k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation
13 months ago davidhillis • 0
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464
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
14 months ago therealgenna • 0
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3
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1.0k
views
Add GP values to VCF
VariantAnnotation
15 months ago Stephanie M. Gogarten ▴ 870
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1
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1.5k
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Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 17 months ago by 65k • written 17 months ago by ▴ 30
2
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4
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933
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
19 months ago rwan.work • 0
0
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2
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734
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
19 months ago rwan.work • 0
0
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2
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2.6k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.3 years ago by ▴ 870
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3
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999
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.2 years ago by • 0 • written 2.3 years ago by • 0
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2
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1.0k
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Reading vcf file with readVcf
VariantAnnotation
2.6 years ago aurelien.dejode • 0
0
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2
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806
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Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 2.7 years ago by 16k • written 2.8 years ago by • 0
0
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5
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1.3k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 2.7 years ago by 6.7k • written 2.7 years ago by • 0
0
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1
reply
874
views
GRanges object out-of-bound
VariantAnnotation
updated 2.7 years ago by 6.7k • written 2.8 years ago by • 0
2
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3
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1.1k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 3 months ago by • 0 • written 2.8 years ago by ▴ 470
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0
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596
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
2.8 years ago Kasper_holm2 • 0
0
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4
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1.5k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
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2
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1.2k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
0
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2
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2.2k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3.1 years ago by 6.7k • written 3.1 years ago by • 0
1
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12
replies
3.0k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.1 years ago by 6.7k • written 3.1 years ago by • 0
0
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2
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1.2k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
3.1 years ago naive • 0
2
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2
replies
1.2k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 3.8 years ago by 25k • written 3.8 years ago by ★ 1.5k
3
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2
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1.3k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 4.0 years ago by 25k • written 4.0 years ago by ★ 1.5k
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2
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1.1k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 4.1 years ago by 25k • written 4.1 years ago by • 0
0
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1
reply
650
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
0
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1
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1.2k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
2
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3
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1.5k
views
"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
GenomicRanges rtracklayer VariantAnnotation S4Vectors SummarizedExperiment
updated 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 30
2
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3
replies
937
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 4.8 years ago by ★ 11k • written 4.8 years ago by • 0
0
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1
reply
764
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 4.9 years ago by ★ 11k • written 4.9 years ago by • 0
0
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3
replies
1.0k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
4.9 years ago Dario Strbenac ★ 1.5k
0
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0
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763
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predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 5.1 years ago by 3.8k • written 5.1 years ago by • 0
2
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3
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1.4k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 5.1 years ago by ★ 6.8k • written 5.1 years ago by ▴ 20
3
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8
replies
3.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
5.1 years ago daniel.magnus.bader ▴ 40
0
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1
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933
views
VariantAnnotation fails to load VCF record
variantannotation
5.4 years ago Daniel Cameron ▴ 40
0
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6
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1.5k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 5.4 years ago by ▴ 30 • written 5.4 years ago by • 0
0
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1
reply
827
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 5.4 years ago by ★ 6.8k • written 5.4 years ago by ▴ 20
1
vote
7
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3.1k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 5.6 years ago by ★ 6.8k • written 5.6 years ago by ▴ 10
3
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3
replies
1.3k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 5.8 years ago by ★ 6.8k • written 5.8 years ago by ▴ 10
3
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4
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1.7k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 5.8 years ago by ★ 11k • written 5.8 years ago by • 0
0
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2
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1.2k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 5.8 years ago by ★ 6.8k • written 5.8 years ago by • 0
0
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2
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1.2k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
5.9 years ago Vivek.b ▴ 100
0
votes
2
replies
1.5k
views
filtering a VCF file based on genotype
variantannotation
updated 5.9 years ago by ★ 6.8k • written 6.0 years ago by ▴ 670
0
votes
1
reply
1.2k
views
VariantAnnotation and filtering a VCF
variantannotation
6.0 years ago Bogdan ▴ 670
0
votes
1
reply
1.1k
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
6.1 years ago sandmann.t ▴ 70
2
votes
2
replies
1.4k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 6.4 years ago by ★ 6.8k • written 6.4 years ago by ▴ 660
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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