Showing : VariantAnnotation • reset
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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 10.7 years ago by ★ 6.8k • written 10.7 years ago by • 0
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10
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3.2k
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predictCoding error DNAStringSet_translate
variantannotation predict coding
updated 10.7 years ago by ★ 6.8k • written 10.7 years ago by ▴ 40
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5
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2.6k
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Error installing VariantAnnotation with bioconductor/devel_core
install variantannotation
10.7 years ago kforner • 0
4
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4
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2.6k
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readVcfAsVRanges + FilterRules
variantannotation filterVcf readvcfasvranges filterRules
updated 10.8 years ago by 25k • written 10.8 years ago by ▴ 50
2
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3
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3.0k
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Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation vranges readvcf readvcfasvranges metadata
10.8 years ago summerela • 0
3
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5
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3.9k
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Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation granges DNAStringSetList findoverlaps Vranges
10.8 years ago summerela • 0
4
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6
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2.4k
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VariantAnnotation non-model species
variantannotation
10.8 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
3
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2
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1.7k
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VariantAnnotation package, subseting vcfs on fixed fields
variantannotation vcf fixed filter
10.9 years ago Anna N. • 0
2
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2
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1.9k
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promoter definition in VariantAnnotation
VariantAnnotation promoter drosophila melanogaster
updated 10.9 years ago by ★ 6.8k • written 10.9 years ago by ▴ 30
4
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11
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2.6k
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Filter every X position
variantannotation
11.0 years ago • updated 10.9 years ago remi.tournebize ▴ 10
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5
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2.7k
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VariantAnnotation _ problem in merging files, mutationspectrum per sample
variantannotation
updated 11.0 years ago by ★ 1.3k • written 11.0 years ago by • 0
2
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4
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2.2k
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Memory usage in readVcf from VariantAnnotation
VariantAnnotation
11.0 years ago Kasper Daniel Hansen ★ 6.5k
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12
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3.5k
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VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation readvcf readgt
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by ▴ 150
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1.8k
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readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation vcf readvcf variantannotation
11.0 years ago jls2282 • 0
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2
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1.6k
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How to correct VCF Iranges from width=1 to correct end coordinate
VCF iranges End software error variantannotation
11.0 years ago tiffanie.moss • 0
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2
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2.8k
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VariantAnnotation Installation Error RSQLite
VariantAnnotation RSQLite
11.0 years ago remi.tournebize ▴ 10
3
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4
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4.4k
views
Quality filtering of exactSNP-generated VCF files
exactSNP qc variantannotation
updated 11.1 years ago by ★ 3.6k • written 11.1 years ago by ▴ 100
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10
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3.7k
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Incorrect row names when a VCF has multiple ALTs.
variantannotation vcf
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by • 0
7
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5
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1.7k
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writeVcf no longer writes records for ungenotyped data
variantannotation
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by ▴ 40
2
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3
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1.7k
views
readVcf skipping CS field in INFO
variantannotation readVcf
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by ▴ 760
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5
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2.3k
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VariantAnnotation VCF read error
variantannotation readvcf
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by ▴ 10
2
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6
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4.0k
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Import of vcf with VariantAnnotation
variantannotation somaticsignatures
11.1 years ago Anna N. • 0
3
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2
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5.4k
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Add data to Vcf Info Field
variantannotation
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by ▴ 50
0
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1
reply
1.4k
views
predictCoding function in VariantAnnotation packages
variantannotation
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by • 0
2
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2
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2.8k
views
Vranges (somatic signature) VariantAnnotation
software error variantannotation
updated 11.1 years ago by ★ 13k • written 11.1 years ago by • 0
4
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3
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2.0k
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how to save file on local disk after applying predictCoding() function?
vcf predict coding save file VariantAnnotation
updated 11.2 years ago by ▴ 90 • written 11.2 years ago by ▴ 10
2
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1
reply
2.3k
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'seqlevels(seqinfo(x))' and 'levels(seqnames(x))' are not identical
variantannotation seqlevels error
updated 11.2 years ago by ★ 6.8k • written 11.2 years ago by ▴ 290
0
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8
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3.6k
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Best practices to find intersection among variants
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 11.3 years ago by ★ 1.3k • written 11.3 years ago by ▴ 220
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0
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1.1k
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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation Annotation GenomicRanges VariantAnnotation GenomicAlignments Annotation
11.3 years ago Valerie Obenchain ★ 6.8k
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5
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1.6k
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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation GenomicRanges VariantAnnotation VariantAnnotation GenomicRanges
updated 11.4 years ago by ★ 3.4k • written 11.4 years ago by ★ 6.8k
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2
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1.7k
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DNAStringSet_translate error in predictCoding()
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 11.5 years ago by ★ 6.8k • written 11.5 years ago by ▴ 20
0
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7
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2.2k
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mutant allele read counts
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 11.5 years ago by ★ 6.8k • written 11.5 years ago by ★ 13k
0
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1
reply
2.8k
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help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
SNP VariantAnnotation Annotation probe VariantAnnotation GWASTools SNP VariantAnnotation
updated 11.5 years ago by ▴ 890 • written 11.5 years ago by ▴ 160
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1
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4.1k
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Multi-sample VCF file and filterVcf
VariantAnnotation Annotation VariantAnnotation VariantAnnotation Annotation VariantAnnotation
updated 11.6 years ago by ★ 6.8k • written 11.6 years ago by ★ 13k
0
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3
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1.6k
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VariantAnnotation - extracting AD and PL fields
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 11.7 years ago by ★ 11k • written 11.7 years ago by ▴ 20
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2
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4.4k
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VariantAnnotation R Package - Merging Two VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.8 years ago by ▴ 320
0
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9
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2.6k
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variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 11.8 years ago by 16k • written 11.8 years ago by ▴ 740
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5
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2.5k
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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
BiocViews VariantAnnotation Annotation biocViews Rsubread VariantAnnotation gmapR BiocViews
12.0 years ago • updated 11.9 years ago Thomas Girke ★ 1.7k
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11
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2.9k
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Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
VariantAnnotation Annotation VariantAnnotation VariantTools VariantAnnotation Annotation
updated 12.0 years ago by ★ 6.8k • written 12.0 years ago by ★ 1.7k
0
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0
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1.6k
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zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
12.0 years ago Valerie Obenchain ★ 6.8k
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2
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1.3k
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readVcf fails when ALT field contains breakends and no symbolic allele
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.1 years ago by ▴ 40 • written 12.1 years ago by ★ 6.8k
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2
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1.3k
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stranded intronic variants with VariantAnnotation::locateVariants()
VariantAnnotation Annotation VariantAnnotation VariantAnnotation Annotation VariantAnnotation
updated 12.1 years ago by ★ 6.8k • written 12.1 years ago by ★ 3.4k
0
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3
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1.3k
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Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
12.2 years ago Michael Lawrence ★ 11k
0
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0
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989
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Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
12.2 years ago Michael Lawrence ★ 11k
0
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2
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1.9k
views
Error in locateVariants
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.4 years ago by ★ 6.8k • written 12.4 years ago by ▴ 10
0
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4
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2.6k
views
'namespace:Biostrings' error when installing VariantAnnotation
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ▴ 20
0
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7
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3.8k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation PROcess Rsamtools VariantAnnotation VariantAnnotation PROcess Rsamtools
updated 12.6 years ago by 6.7k • written 12.6 years ago by ▴ 300
0
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5
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2.1k
views
VariantAnnotation and distance to genes
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.6 years ago by 68k • written 12.6 years ago by ▴ 20
0
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2
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3.6k
views
Problem reading VCF file using readVcf from package VariantAnnotation
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.6 years ago by ★ 6.8k • written 12.6 years ago by ▴ 300
0
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3
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1.6k
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writeVcf bug
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.6 years ago by ★ 6.8k • written 12.6 years ago by ▴ 80
217 results • Page 4 of 5
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Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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