Showing : VariantAnnotation • reset
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
1 day ago • updated 6 hours ago Marco • 0
0
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1
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381
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 5 months ago by 6.7k • written 5 months ago by • 0
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440
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
7 months ago ramiro.barrantes ▴ 10
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2
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1.3k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 9 months ago by 52k • written 9 months ago by • 0
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416
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
10 months ago Stevie Pederson • 0
0
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1
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476
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Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 11 months ago by 68k • written 11 months ago by ▴ 180
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0
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385
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
13 months ago Vincent J. Carey, Jr. 6.7k
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5
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897
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 15 months ago by 68k • written 15 months ago by ▴ 70
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936
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
17 months ago Bogdan ▴ 670
2
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2
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1.8k
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Matching Variants Between Two VCF Objects
VariantAnnotation
written 4.3 years ago by ★ 1.6k
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2
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893
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 21 months ago by ★ 4.7k • written 21 months ago by • 0
4
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8
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2.3k
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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
23 months ago davidhillis • 0
0
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762
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.0 years ago therealgenna • 0
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3
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1.6k
views
Add GP values to VCF
VariantAnnotation
2.1 years ago Stephanie M. Gogarten ▴ 890
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1
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2.2k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 30
2
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4
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1.4k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.5 years ago rwan.work • 0
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2
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1.1k
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Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.5 years ago rwan.work • 0
0
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2
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3.0k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 12.1 years ago by ▴ 890
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3
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1.3k
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Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.0 years ago by • 0 • written 3.2 years ago by • 0
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2
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1.5k
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Reading vcf file with readVcf
VariantAnnotation
3.4 years ago aurelien.dejode • 0
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2
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1.1k
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Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 3.5 years ago by 16k • written 3.6 years ago by • 0
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5
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1.8k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 3.5 years ago by 6.7k • written 3.5 years ago by • 0
0
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1
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1.2k
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GRanges object out-of-bound
VariantAnnotation
updated 3.5 years ago by 6.7k • written 3.6 years ago by • 0
2
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3
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1.3k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 13 months ago by • 0 • written 3.6 years ago by ▴ 470
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0
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787
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.6 years ago Kasper_holm2 • 0
0
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4
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2.2k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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2
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1.5k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
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2
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2.9k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3.9 years ago by 6.7k • written 4.0 years ago by • 0
1
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12
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4.0k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.9 years ago by 6.7k • written 4.0 years ago by • 0
0
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2
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1.7k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4.0 years ago naive • 0
2
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4
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1.7k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 4.7 years ago by ★ 1.6k
3
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2
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1.7k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 4.9 years ago by 25k • written 4.9 years ago by ★ 1.6k
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2
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1.5k
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Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
0
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1
reply
850
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
0
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1
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1.6k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
2
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3
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1.9k
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 5.6 years ago by ★ 13k • written 5.6 years ago by ▴ 30
2
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3
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1.3k
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 5.6 years ago by ★ 11k • written 5.6 years ago by • 0
0
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1
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1.0k
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negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 5.7 years ago by ★ 11k • written 5.7 years ago by • 0
0
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3
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1.3k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
5.7 years ago Dario Strbenac ★ 1.6k
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0
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974
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predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 5.9 years ago by 4.1k • written 5.9 years ago by • 0
2
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3
replies
1.8k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 6.0 years ago by ★ 6.8k • written 6.0 years ago by ▴ 20
4
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9
replies
4.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 9 months ago by • 0 • written 6.0 years ago by ▴ 50
0
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1
reply
1.1k
views
VariantAnnotation fails to load VCF record
variantannotation
6.2 years ago Daniel Cameron ▴ 40
0
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6
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1.9k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.3 years ago by ▴ 30 • written 6.3 years ago by • 0
0
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1
reply
1.1k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 6.3 years ago by ★ 6.8k • written 6.3 years ago by ▴ 20
1
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7
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3.8k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.4 years ago by ★ 6.8k • written 6.4 years ago by ▴ 10
3
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3
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1.5k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 6.7 years ago by ★ 6.8k • written 6.7 years ago by ▴ 10
3
votes
4
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2.1k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.7 years ago by ★ 11k • written 6.7 years ago by • 0
0
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2
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1.4k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 6.7 years ago by ★ 6.8k • written 6.7 years ago by • 0
0
votes
2
replies
1.5k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.8 years ago Vivek.b ▴ 100
50 results • Page 1 of 1
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Comment: Problem using locateVariants() from the VariantAnnotation package by Marco • 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
Comment: Conumee for EPIC and EPICv2 copy number by Adam • 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This post does not fit the theme of this forum.
Comment: Unbalanced experiment with multiple samples from each patient. by canarias • 0
Hi Aaron, I'm faced with an analysis that has basically the same problem as OP had, but is probably even more unbalanced: In most cases, I…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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