Showing : variantAnnotation • reset
1
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2
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249
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 10 days ago by 51k • written 13 days ago by • 0
0
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0
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122
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
8 weeks ago Stevie Pederson • 0
0
votes
1
reply
187
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 3 months ago by 66k • written 3 months ago by ▴ 180
0
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0
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189
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
5 months ago Vincent J. Carey, Jr. 6.7k
0
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5
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548
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 6 months ago by 66k • written 6 months ago by ▴ 50
0
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0
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517
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
8 months ago Bogdan ▴ 670
2
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2
replies
1.5k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.6 years ago by ★ 1.5k
0
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2
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586
views
Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 13 months ago by ★ 4.2k • written 13 months ago by • 0
4
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8
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1.6k
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
15 months ago davidhillis • 0
0
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0
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539
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
16 months ago therealgenna • 0
0
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3
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1.1k
views
Add GP values to VCF
VariantAnnotation
17 months ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
1.6k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 19 months ago by 66k • written 19 months ago by ▴ 30
2
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4
replies
997
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
21 months ago rwan.work • 0
0
votes
2
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789
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
21 months ago rwan.work • 0
0
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2
replies
2.6k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.4 years ago by ▴ 870
0
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3
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1.1k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.3 years ago by • 0 • written 2.4 years ago by • 0
0
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2
replies
1.1k
views
Reading vcf file with readVcf
VariantAnnotation
2.7 years ago aurelien.dejode • 0
0
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2
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843
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 2.8 years ago by 16k • written 2.9 years ago by • 0
0
votes
5
replies
1.4k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 2.8 years ago by 6.7k • written 2.8 years ago by • 0
0
votes
1
reply
922
views
GRanges object out-of-bound
VariantAnnotation
updated 2.8 years ago by 6.7k • written 2.9 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 4 months ago by • 0 • written 2.9 years ago by ▴ 470
0
votes
0
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622
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
2.9 years ago Kasper_holm2 • 0
0
votes
4
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1.7k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3.0 years ago by 66k • written 3.0 years ago by • 0
0
votes
2
replies
1.2k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 3.1 years ago by 66k • written 3.1 years ago by • 0
0
votes
2
replies
2.3k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3.2 years ago by 6.7k • written 3.3 years ago by • 0
1
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12
replies
3.1k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.2 years ago by 6.7k • written 3.2 years ago by • 0
0
votes
2
replies
1.3k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
3.2 years ago naive • 0
2
votes
2
replies
1.3k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 4.0 years ago by 25k • written 4.0 years ago by ★ 1.5k
3
votes
2
replies
1.4k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 4.1 years ago by 25k • written 4.1 years ago by ★ 1.5k
0
votes
2
replies
1.2k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 4.2 years ago by 25k • written 4.2 years ago by • 0
0
votes
1
reply
681
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 4.4 years ago by 66k • written 4.4 years ago by • 0
0
votes
1
reply
1.2k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 4.7 years ago by 25k • written 4.7 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 4.9 years ago by ★ 13k • written 4.9 years ago by ▴ 30
2
votes
3
replies
994
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 4.9 years ago by ★ 11k • written 4.9 years ago by • 0
0
votes
1
reply
794
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 5.0 years ago by ★ 11k • written 5.0 years ago by • 0
0
votes
3
replies
1.1k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
5.0 years ago Dario Strbenac ★ 1.5k
0
votes
0
replies
797
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 5.2 years ago by 3.9k • written 5.2 years ago by • 0
2
votes
3
replies
1.5k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 5.2 years ago by ★ 6.8k • written 5.3 years ago by ▴ 20
4
votes
9
replies
3.2k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 29 days ago by • 0 • written 5.3 years ago by ▴ 50
0
votes
1
reply
961
views
VariantAnnotation fails to load VCF record
variantannotation
5.5 years ago Daniel Cameron ▴ 40
0
votes
6
replies
1.6k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 5.5 years ago by ▴ 30 • written 5.5 years ago by • 0
0
votes
1
reply
853
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 5.6 years ago by ★ 6.8k • written 5.6 years ago by ▴ 20
1
vote
7
replies
3.2k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 5.7 years ago by ★ 6.8k • written 5.7 years ago by ▴ 10
3
votes
3
replies
1.3k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 5.9 years ago by ★ 6.8k • written 6.0 years ago by ▴ 10
3
votes
4
replies
1.7k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 5.9 years ago by ★ 11k • written 5.9 years ago by • 0
0
votes
2
replies
1.2k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 6.0 years ago by ★ 6.8k • written 6.0 years ago by • 0
0
votes
2
replies
1.3k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.0 years ago Vivek.b ▴ 100
0
votes
2
replies
1.6k
views
filtering a VCF file based on genotype
variantannotation
updated 6.1 years ago by ★ 6.8k • written 6.1 years ago by ▴ 670
0
votes
1
reply
1.2k
views
VariantAnnotation and filtering a VCF
variantannotation
6.1 years ago Bogdan ▴ 670
0
votes
1
reply
1.1k
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
6.3 years ago sandmann.t ▴ 70
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for looking into this and for your explanation! As a follow-up, would it be possible in future releases of featureCounts to pro…
Comment: error loading collectTRI regulon by silvaesilva.da • 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate by James W. MacDonald 66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Answer: Limma model.matrix design with batch effect and different life stages proportion by Masongeorge • 0
Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.
Comment: error loading collectTRI regulon by deeenes ▴ 50
I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…
Votes
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Answer: DESeq2 returns results for group with just one replicate
Answer: DESeq2 returns results for group with just one replicate
Comment: error loading collectTRI regulon
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