Showing : VCF • reset
0
votes
0
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479
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
14 months ago therealgenna • 0
0
votes
0
replies
503
views
Prepare data frame of 3 column-lists or matrix of three-column lists from VCF or BAM files
BAM Segmentation CINdex VCF Data
20 months ago raven1306 • 0
2
votes
1
reply
2.5k
views
merge vcf files with different samples and variants?
vcf
written 7.2 years ago by ▴ 40
1
vote
2
replies
2.6k
views
Any tool to calculate Fst on haploid data?
snps VCF
updated 24 months ago by • 0 • written 7.2 years ago by ▴ 10
0
votes
2
replies
1.8k
views
How to convert .CEL file to .VCF file?
vcf cell affymetrix
2.9 years ago jesus • 0
0
votes
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
2
votes
2
replies
5.7k
views
how to import/read .vcf files in R
vcf
4.3 years ago anamarija ▴ 10
0
votes
1
reply
789
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf snv gatk customprodb inputvcf
4.8 years ago Elena.M • 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
1
vote
7
replies
1.2k
views
Help creating VRange object
vcf somaticSignatures Vrange
updated 5.0 years ago by ★ 1.3k • written 5.0 years ago by • 0
1
vote
1
reply
1.6k
views
VCF file does not include snp.id, can I still run SNPRelate for Relatedness Analysis? Data is output from STACKS for mangroves
SNPRelate VCF
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by • 0
0
votes
1
reply
995
views
Bioconductor and WGS: recommended practices?
whole genome sequencing variants vcf WGS
5.2 years ago Vincent J. Carey, Jr. 6.7k
0
votes
0
replies
1.2k
views
vcf to venn diagram
snps vcf venn diagram ggplot2
5.4 years ago mictadlo ▴ 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
1
reply
1.5k
views
comparing 2 long BED files in R in an efficient way
bed vcf
updated 5.8 years ago by • 0 • written 5.8 years ago by ▴ 670
2
votes
5
replies
2.5k
views
Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
motifbreakR vcf snps motif analysis
updated 5.9 years ago by ★ 6.8k • written 5.9 years ago by ▴ 830
0
votes
2
replies
1.3k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
1
reply
1.8k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Error converting vcf to gds
snprelate vcf gds
updated 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
2
votes
5
replies
2.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
6.8 years ago Didi ▴ 10
5
votes
6
replies
2.3k
views
extracting Allele Read Counts
rsamtools vcf
7.1 years ago Bogdan ▴ 670
2
votes
3
replies
4.0k
views
Select specific variants from vcf file
vcf
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
0
votes
1
reply
1.1k
views
Error in matrix
bioconductor vcf
7.1 years ago bkauf • 0
4
votes
6
replies
4.2k
views
about collapsed and expanded vcf file
vcf
updated 7.3 years ago by • 0 • written 7.3 years ago by ▴ 670
2
votes
4
replies
1.9k
views
Best way to create a VRanges object from a large VCF file?
variantannotation readvcf readvcfasvranges vcf
updated 7.3 years ago by ★ 11k • written 7.3 years ago by • 0
3
votes
2
replies
1.5k
views
about the use of subsetByFilter()
vcf
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 670
1
vote
5
replies
1.6k
views
about filtering variants from a VCF file
vcf
7.3 years ago Bogdan ▴ 670
3
votes
3
replies
1.2k
views
CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
variantannotation VCF
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by 21k
0
votes
1
reply
1.1k
views
vcfR package vector length error
vcf
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 70
0
votes
4
replies
1.3k
views
annotating a vcf file containing Structural Variants
vcf
7.6 years ago Bogdan ▴ 670
2
votes
2
replies
1.3k
views
readVCFAsVRanges in VariantAnnotation broken by an FTZ format?
variantannotation readvcfasvranges vcf
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 120
1
vote
2
replies
1.2k
views
Expand annotation on a vcf file
vcf variantannotation
updated 7.8 years ago by ★ 11k • written 7.8 years ago by • 0
0
votes
2
replies
1.6k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R variantannotation vcf scanvcfparam readvcf
updated 7.9 years ago by ★ 11k • written 7.9 years ago by • 0
1
vote
1
reply
1.3k
views
Genome versions of the VcfFiles from AnnotationHub
annotation software error vcf annotationhub
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ▴ 10
0
votes
1
reply
3.7k
views
Subset VCF files using multiple criteria
vcf variantannotation granges
8.2 years ago georgewwp • 0
0
votes
3
replies
2.2k
views
vcf postion extract
vcf variantannotation position
updated 8.3 years ago by 25k • written 8.3 years ago by • 0
0
votes
4
replies
2.7k
views
How to import vcf with multi sample?
vcf readvcf readvcfasvranges
8.4 years ago Marcin Grzybowski • 0
2
votes
5
replies
2.5k
views
Plot data from VCF using Gviz?
gviz variantannotation vcf
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by ★ 2.0k
2
votes
3
replies
1.2k
views
genotypeToSnpMatrix doesn't handle PL
variantannotation vcf
updated 8.5 years ago by ▴ 870 • written 8.5 years ago by ▴ 80
3
votes
8
replies
1.7k
views
problem with @ranges@start in DNAStringSet
vcf testthat dnastringset
8.5 years ago TimothéeFlutre ▴ 80
2
votes
2
replies
1.4k
views
a filter works alone but not with other filters
variantannotation vcf filtervcf
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 80
5
votes
2
replies
1.1k
views
filter "isSnp" for VCF
variantannotation filtervcf vcf
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ▴ 80
0
votes
2
replies
1.5k
views
filterVcf: error with param argument
VariantAnnotation filterVcf ScanVcfParam vcf writeVcf
updated 8.7 years ago by 25k • written 8.7 years ago by • 0
2
votes
1
reply
1.4k
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf vcf tabix
updated 8.8 years ago by ★ 6.8k • written 8.8 years ago by ▴ 50
0
votes
2
replies
1.3k
views
Problem with Annotating Genomic Variant
workflows vcf
8.9 years ago merella.stefania • 0
2
votes
9
replies
2.7k
views
ReadVCF not reading samples
readvcf vcf variantannotation
9.0 years ago askates ▴ 10
7
votes
3
replies
1.2k
views
Extracting first member of each element of a matrix of lists
variantannotation vcf
updated 9.0 years ago by ★ 11k • written 9.0 years ago by 21k
0
votes
0
replies
1.7k
views
Producing alternate protein sequences from VCF
protein vcf
9.0 years ago dan.gatti • 0
0
votes
4
replies
4.7k
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 9.1 years ago by ★ 6.8k • written 9.1 years ago by • 0
3
votes
2
replies
1.3k
views
VariantAnnotation package, subseting vcfs on fixed fields
variantannotation vcf fixed filter
9.3 years ago Anna N. • 0
50 results • Page 1 of 1
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Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
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Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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