Showing : variantannotation • reset
1
vote
4
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5.9k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.7 years ago by ★ 6.8k
1
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2
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5.1k
views
ICU init failed: U_FILE_ACCESS_ERROR while loading library "VariantAnnotation"
variantannotation library error
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by ▴ 50
3
votes
2
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5.0k
views
Add data to Vcf Info Field
variantannotation
updated 10.0 years ago by ★ 6.8k • written 10.0 years ago by ▴ 50
0
votes
4
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5.0k
views
Question: How can I filter a vcf file by DP and GQ using the R package VariantAnnotation?
VariantAnnotation Sample Read Depth Phred-Scaled Genotype Quality vcf
updated 9.6 years ago by ★ 6.8k • written 9.6 years ago by • 0
0
votes
21
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4.7k
views
VariantAnnotation Errors and void outputs
variantannotation readvcf
9.4 years ago pifferdavide • 0
1
vote
5
replies
4.6k
views
Converting a DNAStringSetList to characters quickly
readVcf DNAStringSet DNAStringSetList variantannotation readvcf
9.5 years ago dan.gatti • 0
0
votes
2
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4.1k
views
VariantAnnotation R Package - Merging Two VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 10.7 years ago by ▴ 320
3
votes
4
replies
3.9k
views
Quality filtering of exactSNP-generated VCF files
exactSNP qc variantannotation
updated 9.9 years ago by ★ 3.6k • written 9.9 years ago by ▴ 100
0
votes
1
reply
3.9k
views
Subset VCF files using multiple criteria
vcf variantannotation granges
8.7 years ago georgewwp • 0
0
votes
1
reply
3.6k
views
Multi-sample VCF file and filterVcf
VariantAnnotation Annotation VariantAnnotation VariantAnnotation Annotation VariantAnnotation
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ★ 13k
4
votes
9
replies
3.6k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 5 months ago by • 0 • written 5.6 years ago by ▴ 50
1
vote
12
replies
3.5k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.5 years ago by 6.7k • written 3.6 years ago by • 0
2
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6
replies
3.5k
views
Import of vcf with VariantAnnotation
variantannotation somaticsignatures
10.0 years ago Anna N. • 0
3
votes
9
replies
3.5k
views
Annotate VCFs with Cosmic (ExAC etc.) fields
variantannotation cosmic exac
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 130
1
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7
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3.5k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.0 years ago by ★ 6.8k • written 6.1 years ago by ▴ 10
5
votes
6
replies
3.4k
views
Error in reading 1000 genomes data
variantannotation
updated 8.6 years ago by 25k • written 9.9 years ago by ▴ 20
3
votes
5
replies
3.3k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation granges DNAStringSetList findoverlaps Vranges
9.7 years ago summerela • 0
4
votes
10
replies
3.3k
views
Best way to import from multiple VCF files?
variantannotation
updated 8.2 years ago by 4.0k • written 8.2 years ago by ▴ 150
0
votes
2
replies
3.1k
views
Problem reading VCF file using readVcf from package VariantAnnotation
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 11.5 years ago by ★ 6.8k • written 11.5 years ago by ▴ 300
0
votes
10
replies
3.1k
views
Incorrect row names when a VCF has multiple ALTs.
variantannotation vcf
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by • 0
0
votes
7
replies
3.1k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation PROcess Rsamtools VariantAnnotation VariantAnnotation PROcess Rsamtools
updated 11.4 years ago by 6.7k • written 11.4 years ago by ▴ 300
0
votes
7
replies
3.1k
views
append to bgzipped VCF file
variantannotation tabix
updated 9.0 years ago by ★ 11k • written 9.0 years ago by ▴ 80
1
vote
12
replies
3.0k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation readvcf readgt
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by ▴ 150
0
votes
8
replies
3.0k
views
Best practices to find intersection among variants
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ▴ 220
0
votes
6
replies
3.0k
views
readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantannotation
updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by ▴ 40
2
votes
9
replies
3.0k
views
ReadVCF not reading samples
readvcf vcf variantannotation
9.4 years ago askates ▴ 10
0
votes
2
replies
3.0k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 6.9 years ago by 67k • written 6.9 years ago by ★ 2.0k
0
votes
23
replies
2.9k
views
VariantAnnotation geno function
variantannotation
7.9 years ago ribioinfo ▴ 100
0
votes
17
replies
2.9k
views
problems with strand in predictCoding
VariantAnnotation Annotation BSgenome BSgenome VariantAnnotation VariantAnnotation BSgenome
updated 12.5 years ago by ▴ 20 • written 12.5 years ago by ▴ 50
2
votes
6
replies
2.8k
views
extracting Allele Read Counts - part2
rsamtools variantannotation
updated 7.5 years ago by 67k • written 7.5 years ago by ▴ 670
2
votes
5
replies
2.8k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
7.2 years ago Didi ▴ 10
0
votes
2
replies
2.8k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.8 years ago by ▴ 870
2
votes
5
replies
2.8k
views
Plot data from VCF using Gviz?
gviz variantannotation vcf
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by ★ 2.1k
1
vote
23
replies
2.7k
views
Distance calculation for variants in intergenic regions
locatevariants variantannotation genomicfeatures
updated 7.9 years ago by ★ 11k • written 7.9 years ago by • 0
0
votes
2
replies
2.6k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3.5 years ago by 6.7k • written 3.6 years ago by • 0
0
votes
1
reply
2.6k
views
help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
SNP VariantAnnotation Annotation probe VariantAnnotation GWASTools SNP VariantAnnotation
updated 10.4 years ago by ▴ 870 • written 10.4 years ago by ▴ 160
1
vote
10
replies
2.6k
views
predictCoding error DNAStringSet_translate
variantannotation predict coding
updated 9.6 years ago by ★ 6.8k • written 9.6 years ago by ▴ 40
2
votes
2
replies
2.5k
views
Vranges (somatic signature) VariantAnnotation
software error variantannotation
updated 10.0 years ago by ★ 13k • written 10.0 years ago by • 0
3
votes
3
replies
2.5k
views
VariantAnnotation Installation Failure
VariantAnnotation
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by ▴ 370
0
votes
20
replies
2.5k
views
VariantAnnotation function getTranscriptSeqs() gives error "object '.makeUCSCTxListFromGRangesList' not found"
variantannotation
9.2 years ago • updated 9.0 years ago Tjeerd Dijkstra • 0
0
votes
6
replies
2.5k
views
Error using readVcf
gwastools variantannotation
updated 7.3 years ago by ▴ 870 • written 7.3 years ago by • 0
2
votes
3
replies
2.4k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation vranges readvcf readvcfasvranges metadata
9.7 years ago • updated 9.6 years ago summerela • 0
0
votes
2
replies
2.4k
views
VariantAnnotation Installation Error RSQLite
VariantAnnotation RSQLite
9.9 years ago remi.tournebize ▴ 10
1
vote
4
replies
2.4k
views
variantAnnotation::locateVariants() with AllVariants(): why do some input variants not get annotated?
variantannotation locatevariants
9.1 years ago Jakob Goldmann • 0
0
votes
3
replies
2.4k
views
vcf postion extract
vcf variantannotation position
updated 8.7 years ago by 25k • written 8.7 years ago by • 0
7
votes
4
replies
2.3k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 40
0
votes
5
replies
2.3k
views
VariantAnnotation _ problem in merging files, mutationspectrum per sample
variantannotation
updated 9.8 years ago by ★ 1.3k • written 9.9 years ago by • 0
4
votes
4
replies
2.3k
views
readVcfAsVRanges + FilterRules
variantannotation filterVcf readvcfasvranges filterRules
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 50
1
vote
3
replies
2.2k
views
annotation of SV (Structural Variants)
variantannotation annotationhub
7.6 years ago Bogdan ▴ 670
0
votes
4
replies
2.2k
views
'namespace:Biostrings' error when installing VariantAnnotation
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 11.3 years ago by ★ 13k • written 11.3 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: featureCounts fails to load annotation file by Yang Liao ▴ 440
Hi Yasmin, I'm following up on the issue you're having with featureCounts and the GRCh38 RefSeq annotation. I've been testing featureCounts…
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You are overthinking this. You have two time points, you compare them to each other. You can't compare them to a time point you don't hav…
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As far as I am aware, the restriction is historical..having a fixed buffer size in the internal C methods makes the algorithms a little sim…
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I am facing a similar issue.
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Yes, the current behaviour is absolutely intentional. It doesn't seem to me to be meaningful or useful to try to subset the EList object au…
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C: bumphunter beta values
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Answer: Are transformed values from rlog /vst log2 normalized counts?
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