Showing : vcf • reset
1
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2
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1.9k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 18 months ago by 53k • written 18 months ago by • 0
0
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0
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962
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.8 years ago therealgenna • 0
0
votes
0
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873
views
Prepare data frame of 3 column-lists or matrix of three-column lists from VCF or BAM files
BAM Segmentation CINdex VCF Data
3.3 years ago raven1306 • 0
1
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2
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3.5k
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Any tool to calculate Fst on haploid data?
snps VCF
updated 3.6 years ago by • 0 • written 8.8 years ago by ▴ 10
0
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2
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2.7k
views
How to convert .CEL file to .VCF file?
vcf cell affymetrix
4.5 years ago • updated 4.4 years ago jesus • 0
0
votes
2
replies
1.8k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
2
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2
replies
7.9k
views
how to import/read .vcf files in R
vcf
5.8 years ago anamarija ▴ 10
0
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1
reply
1.3k
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf snv gatk customprodb inputvcf
6.4 years ago Elena.M • 0
0
votes
3
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1.5k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
6.5 years ago Dario Strbenac ★ 1.6k
1
vote
7
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1.9k
views
Help creating VRange object
vcf somaticSignatures Vrange
updated 6.6 years ago by ★ 1.3k • written 6.6 years ago by • 0
1
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1
reply
2.1k
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 6.7 years ago by ▴ 890 • written 6.7 years ago by • 0
0
votes
1
reply
1.4k
views
Bioconductor and WGS: recommended practices?
whole genome sequencing variants vcf WGS
6.8 years ago Vincent J. Carey, Jr. 6.7k
0
votes
0
replies
1.6k
views
vcf to venn diagram
snps vcf venn diagram ggplot2
6.9 years ago mictadlo ▴ 10
3
votes
4
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2.3k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 7.4 years ago by ★ 11k • written 7.4 years ago by • 0
0
votes
1
reply
2.1k
views
comparing 2 long BED files in R in an efficient way
bed vcf
updated 7.4 years ago by • 0 • written 7.4 years ago by ▴ 670
2
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5
replies
3.3k
views
Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
motifbreakR vcf snps motif analysis
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by ▴ 840
0
votes
2
replies
2.0k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN VCF QUAL
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
0
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1
reply
2.3k
views
VCF file non-SNP germline mutations
PureCN VCF SNP
updated 7.6 years ago by ▴ 130 • written 7.6 years ago by ▴ 10
0
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2
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2.1k
views
Error converting vcf to gds
snprelate vcf gds
updated 7.7 years ago by ▴ 30 • written 7.7 years ago by • 0
2
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5
replies
3.4k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
8.3 years ago Didi ▴ 10
5
votes
6
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3.3k
views
extracting Allele Read Counts
rsamtools vcf
8.7 years ago Bogdan ▴ 670
2
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3
replies
5.3k
views
Select specific variants from vcf file
vcf
updated 8.7 years ago by 25k • written 8.7 years ago by • 0
0
votes
1
reply
1.5k
views
Error in matrix
bioconductor vcf
8.7 years ago bkauf • 0
2
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1
reply
2.9k
views
merge vcf files with different samples and variants?
vcf
written 8.7 years ago by ▴ 40
4
votes
6
replies
5.4k
views
about collapsed and expanded vcf file
vcf
updated 8.8 years ago by • 0 • written 8.9 years ago by ▴ 670
2
votes
4
replies
2.7k
views
Best way to create a VRanges object from a large VCF file?
variantannotation readvcf readvcfasvranges vcf
updated 8.9 years ago by ★ 11k • written 8.9 years ago by • 0
3
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2
replies
1.9k
views
about the use of subsetByFilter()
vcf
updated 8.9 years ago by 25k • written 8.9 years ago by ▴ 670
1
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5
replies
2.2k
views
about filtering variants from a VCF file
vcf
8.9 years ago Bogdan ▴ 670
3
votes
3
replies
1.8k
views
CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
variantannotation VCF
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by 21k
0
votes
1
reply
1.5k
views
vcfR package vector length error
vcf
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 80
0
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4
replies
1.8k
views
annotating a vcf file containing Structural Variants
vcf
9.2 years ago Bogdan ▴ 670
2
votes
2
replies
1.7k
views
readVCFAsVRanges in VariantAnnotation broken by an FTZ format?
variantannotation readvcfasvranges vcf
updated 9.3 years ago by ★ 11k • written 9.3 years ago by ▴ 120
1
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2
replies
1.6k
views
Expand annotation on a vcf file
vcf variantannotation
updated 9.4 years ago by ★ 11k • written 9.4 years ago by • 0
0
votes
2
replies
2.1k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R variantannotation vcf scanvcfparam readvcf
updated 9.5 years ago by ★ 11k • written 9.5 years ago by • 0
1
vote
1
reply
1.7k
views
Genome versions of the VcfFiles from AnnotationHub
annotation software error vcf annotationhub
updated 9.6 years ago by ★ 6.8k • written 9.6 years ago by ▴ 10
0
votes
1
reply
4.3k
views
Subset VCF files using multiple criteria
vcf variantannotation granges
9.8 years ago georgewwp • 0
0
votes
3
replies
2.7k
views
vcf postion extract
vcf variantannotation position
updated 9.8 years ago by 25k • written 9.8 years ago by • 0
0
votes
4
replies
3.2k
views
How to import vcf with multi sample?
vcf readvcf readvcfasvranges
9.9 years ago Marcin Grzybowski • 0
2
votes
5
replies
3.1k
views
Plot data from VCF using Gviz?
gviz variantannotation vcf
updated 10.0 years ago by ★ 6.8k • written 10.0 years ago by ★ 2.1k
2
votes
3
replies
1.6k
views
genotypeToSnpMatrix doesn't handle PL
variantannotation vcf
updated 10.1 years ago by ▴ 890 • written 10.1 years ago by ▴ 80
3
votes
8
replies
2.4k
views
problem with @ranges@start in DNAStringSet
vcf testthat dnastringset
10.1 years ago TimothéeFlutre ▴ 80
2
votes
2
replies
1.7k
views
a filter works alone but not with other filters
variantannotation vcf filtervcf
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 80
5
votes
2
replies
1.5k
views
filter "isSnp" for VCF
variantannotation filtervcf vcf
updated 10.1 years ago by ★ 11k • written 10.1 years ago by ▴ 80
0
votes
2
replies
1.9k
views
filterVcf: error with param argument
VariantAnnotation filterVcf ScanVcfParam vcf writeVcf
updated 10.3 years ago by 25k • written 10.3 years ago by • 0
2
votes
1
reply
2.0k
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf vcf tabix
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ▴ 50
0
votes
2
replies
1.7k
views
Problem with Annotating Genomic Variant
workflows vcf
10.4 years ago merella.stefania • 0
2
votes
9
replies
3.7k
views
ReadVCF not reading samples
readvcf vcf variantannotation
10.5 years ago askates ▴ 10
7
votes
3
replies
1.6k
views
Extracting first member of each element of a matrix of lists
variantannotation vcf
updated 10.6 years ago by ★ 11k • written 10.6 years ago by 21k
0
votes
0
replies
2.1k
views
Producing alternate protein sequences from VCF
protein vcf
10.6 years ago dan.gatti • 0
0
votes
4
replies
5.7k
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 10.7 years ago by ★ 6.8k • written 10.7 years ago by • 0
55 results • Page 1 of 2
Recent ...
Replies
Comment: Generalized edgeR functions by Omar • 0
[ragdoll hit](https://ragdollhitstickman.io/) That actually sounds like a reasonable approach, especially if the overlapping intervals repr…
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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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