Showing : variantAnnotation • reset
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353
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
7 months ago Marco • 0
0
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1
reply
588
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 13 months ago by 6.7k • written 13 months ago by • 0
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0
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634
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
15 months ago ramiro.barrantes ▴ 10
1
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2
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1.9k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 16 months ago by 53k • written 16 months ago by • 0
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0
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563
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
18 months ago Stevie Pederson • 0
2
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1
reply
673
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 19 months ago by 68k • written 19 months ago by ▴ 180
0
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0
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502
views
RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
21 months ago Vincent J. Carey, Jr. 6.7k
0
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5
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1.1k
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 23 months ago by 68k • written 23 months ago by ▴ 70
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0
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1.2k
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
2.1 years ago Bogdan ▴ 670
2
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2
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2.0k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 4.9 years ago by ★ 1.6k
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2
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1.1k
views
Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
4
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8
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2.9k
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
2.6 years ago davidhillis • 0
0
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0
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938
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.7 years ago therealgenna • 0
0
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3
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1.9k
views
Add GP values to VCF
VariantAnnotation
2.8 years ago Stephanie M. Gogarten ▴ 890
0
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1
reply
2.8k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 30
2
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4
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1.6k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.1 years ago rwan.work • 0
0
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2
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1.3k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.1 years ago rwan.work • 0
0
votes
2
replies
3.2k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 12.8 years ago by ▴ 890
0
votes
3
replies
1.6k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.6 years ago by • 0 • written 3.8 years ago by • 0
0
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2
replies
1.8k
views
Reading vcf file with readVcf
VariantAnnotation
4.1 years ago aurelien.dejode • 0
0
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2
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1.2k
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 4.2 years ago by 16k • written 4.3 years ago by • 0
0
votes
5
replies
2.1k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 4.2 years ago by 6.7k • written 4.2 years ago by • 0
0
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1
reply
1.4k
views
GRanges object out-of-bound
VariantAnnotation
updated 4.2 years ago by 6.7k • written 4.2 years ago by • 0
2
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3
replies
1.5k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 21 months ago by • 0 • written 4.3 years ago by ▴ 470
0
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0
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880
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
4.3 years ago Kasper_holm2 • 0
0
votes
4
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2.5k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
2
replies
1.7k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
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2
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3.3k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 4.6 years ago by 6.7k • written 4.6 years ago by • 0
1
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12
replies
4.7k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 4.6 years ago by 6.7k • written 4.6 years ago by • 0
0
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2
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2.0k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4.6 years ago naive • 0
2
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4
replies
2.0k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 5.3 years ago by ★ 1.6k
3
votes
2
replies
1.9k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 5.5 years ago by 25k • written 5.5 years ago by ★ 1.6k
0
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2
replies
1.8k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 5.5 years ago by 25k • written 5.5 years ago by • 0
0
votes
1
reply
980
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
votes
1
reply
1.8k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 6.0 years ago by 25k • written 6.0 years ago by • 0
2
votes
3
replies
2.2k
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 6.3 years ago by ★ 13k • written 6.3 years ago by ▴ 30
2
votes
3
replies
1.5k
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 6.3 years ago by ★ 11k • written 6.3 years ago by • 0
0
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1
reply
1.1k
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 6.3 years ago by ★ 11k • written 6.4 years ago by • 0
0
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3
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1.4k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
6.4 years ago Dario Strbenac ★ 1.6k
0
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0
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1.1k
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 6.6 years ago by 4.2k • written 6.6 years ago by • 0
2
votes
3
replies
2.1k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 6.6 years ago by ★ 6.8k • written 6.6 years ago by ▴ 20
4
votes
9
replies
4.5k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 17 months ago by • 0 • written 6.6 years ago by ▴ 50
0
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1
reply
1.3k
views
VariantAnnotation fails to load VCF record
variantannotation
6.9 years ago Daniel Cameron ▴ 40
0
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6
replies
2.2k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.9 years ago by ▴ 30 • written 6.9 years ago by • 0
0
votes
1
reply
1.2k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 6.9 years ago by ★ 6.8k • written 6.9 years ago by ▴ 20
1
vote
7
replies
4.2k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 7.1 years ago by ★ 6.8k • written 7.1 years ago by ▴ 10
3
votes
3
replies
1.8k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by ▴ 10
3
votes
4
replies
2.3k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 7.3 years ago by ★ 11k • written 7.3 years ago by • 0
0
votes
2
replies
1.6k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by • 0
0
votes
2
replies
1.7k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
7.4 years ago Vivek.b ▴ 100
216 results • Page 1 of 5
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Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by dzv20413 • 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments by Erik Wright ▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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