Showing : VariantAnnotation • reset
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77
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
15 days ago Stevie Pederson • 0
0
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1
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143
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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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0
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158
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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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473
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 4 months ago by 65k • written 5 months ago by ▴ 30
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0
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443
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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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539
views
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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468
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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
0
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1
reply
1.5k
views
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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934
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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739
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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1.0k
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
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2
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808
views
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
votes
5
replies
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
votes
1
reply
878
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
replies
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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598
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
2.8 years ago Kasper_holm2 • 0
0
votes
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
replies
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 3.2 years ago by • 0
1
vote
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
replies
1.3k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
3.1 years ago naive • 0
2
votes
2
replies
1.3k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 3.8 years ago by 25k • written 3.8 years ago by ★ 1.5k
3
votes
2
replies
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
replies
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
653
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
reply
1.2k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 4.6 years ago by 25k • written 4.6 years ago by • 0
2
votes
3
replies
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
votes
3
replies
938
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 4.8 years ago by ★ 11k • written 4.8 years ago by • 0
0
votes
1
reply
767
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 4.9 years ago by ★ 11k • written 4.9 years ago by • 0
0
votes
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
replies
765
views
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
votes
3
replies
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
votes
8
replies
3.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
5.2 years ago • updated 5.1 years ago daniel.magnus.bader ▴ 40
0
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1
reply
935
views
VariantAnnotation fails to load VCF record
variantannotation
5.4 years ago Daniel Cameron ▴ 40
0
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6
replies
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
votes
1
reply
830
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
replies
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
votes
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
votes
4
replies
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
votes
2
replies
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
votes
2
replies
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
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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