Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
vcf
•
reset
0
votes
0
replies
459
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
489
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
1
vote
2
replies
2.5k
views
Any tool to calculate Fst on haploid data?
snps
VCF
updated 23 months ago by
Arafat
• 0 • written 7.2 years ago by
rkdonthu
▴ 10
0
votes
2
replies
1.7k
views
How to convert .CEL file to .VCF file?
vcf
cell
affymetrix
2.8 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 4.0 years ago by
Martin Morgan
25k • written 4.0 years ago by
W. van Rengs
• 0
2
votes
2
replies
5.7k
views
how to import/read .vcf files in R
vcf
4.2 years ago
anamarija
▴ 10
0
votes
1
reply
766
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
1.1k
views
Help creating VRange object
vcf
somaticSignatures
Vrange
updated 4.9 years ago by
Julian Gehring
★ 1.3k • written 5.0 years ago by
maisapinheiro12
• 0
1
vote
1
reply
1.5k
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
Stephanie M. Gogarten
▴ 870 • written 5.1 years ago by
cav3gh
• 0
0
votes
1
reply
983
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
5.3 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
Michael Lawrence
★ 11k • written 5.8 years ago by
david.mas
• 0
0
votes
1
reply
1.4k
views
comparing 2 long BED files in R in an efficient way
bed
vcf
updated 5.8 years ago by
GENOMIC_region
• 0 • written 5.8 years ago by
Bogdan
▴ 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 5.8 years ago by
Valerie Obenchain
★ 6.8k • written 5.8 years ago by
svlachavas
▴ 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
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
1
reply
1.8k
views
VCF file non-SNP germline mutations
PureCN
VCF
SNP
updated 6.0 years ago by
markus.riester
▴ 130 • written 6.0 years ago by
twtoal
▴ 10
0
votes
2
replies
1.5k
views
Error converting vcf to gds
snprelate
vcf
gds
updated 6.1 years ago by
zhengx
▴ 30 • written 6.1 years ago by
annat22
• 0
2
votes
5
replies
2.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
6.7 years ago
Didi
▴ 10
5
votes
6
replies
2.3k
views
extracting Allele Read Counts
rsamtools
vcf
7.0 years ago
Bogdan
▴ 670
2
votes
3
replies
4.0k
views
Select specific variants from vcf file
vcf
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
Adam
• 0
0
votes
1
reply
1.1k
views
Error in matrix
bioconductor
vcf
7.1 years ago
bkauf
• 0
2
votes
1
reply
2.4k
views
merge vcf files with different samples and variants?
vcf
written 7.1 years ago by
shilin.zhao
▴ 40
4
votes
6
replies
4.2k
views
about collapsed and expanded vcf file
vcf
updated 7.2 years ago by
raggieapauly
• 0 • written 7.3 years ago by
Bogdan
▴ 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
Michael Lawrence
★ 11k • written 7.3 years ago by
ruben.drews
• 0
3
votes
2
replies
1.5k
views
about the use of subsetByFilter()
vcf
updated 7.3 years ago by
Martin Morgan
25k • written 7.3 years ago by
Bogdan
▴ 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 7.3 years ago by
Valerie Obenchain
★ 6.8k • written 7.3 years ago by
Sean Davis
21k
0
votes
1
reply
1.1k
views
vcfR package vector length error
vcf
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
jenniewoo
▴ 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 7.7 years ago by
Michael Lawrence
★ 11k • written 7.7 years ago by
Andy Lynch
▴ 120
1
vote
2
replies
1.2k
views
Expand annotation on a vcf file
vcf
variantannotation
updated 7.8 years ago by
Michael Lawrence
★ 11k • written 7.8 years ago by
Dee
• 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
Michael Lawrence
★ 11k • written 7.9 years ago by
emily.mccann
• 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
Valerie Obenchain
★ 6.8k • written 8.0 years ago by
sskimb
▴ 10
0
votes
1
reply
3.6k
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 8.2 years ago by
Martin Morgan
25k • written 8.2 years ago by
1000G_Q
• 0
0
votes
4
replies
2.7k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
8.3 years ago
Marcin Grzybowski
• 0
2
votes
5
replies
2.5k
views
Plot data from VCF using Gviz?
gviz
variantannotation
vcf
updated 8.4 years ago by
Valerie Obenchain
★ 6.8k • written 8.4 years ago by
Johannes Rainer
★ 2.0k
2
votes
3
replies
1.2k
views
genotypeToSnpMatrix doesn't handle PL
variantannotation
vcf
updated 8.4 years ago by
Stephanie M. Gogarten
▴ 870 • written 8.5 years ago by
TimothéeFlutre
▴ 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
1.3k
views
a filter works alone but not with other filters
variantannotation
vcf
filtervcf
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
TimothéeFlutre
▴ 80
5
votes
2
replies
1.1k
views
filter "isSnp" for VCF
variantannotation
filtervcf
vcf
updated 8.5 years ago by
Michael Lawrence
★ 11k • written 8.5 years ago by
TimothéeFlutre
▴ 80
0
votes
2
replies
1.5k
views
filterVcf: error with param argument
VariantAnnotation
filterVcf
ScanVcfParam
vcf
writeVcf
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
pau.puigdevall
• 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
Valerie Obenchain
★ 6.8k • written 8.8 years ago by
Simon Coetzee
▴ 50
0
votes
2
replies
1.3k
views
Problem with Annotating Genomic Variant
workflows
vcf
8.8 years ago
merella.stefania
• 0
2
votes
9
replies
2.7k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
8.9 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
Michael Lawrence
★ 11k • written 9.0 years ago by
Sean Davis
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
4.6k
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
Valerie Obenchain
★ 6.8k • written 9.1 years ago by
r.jaffe
• 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
Recent ...
Replies
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards
• All
Popular Question
to
James W. MacDonald
65k
Popular Question
to
shepherl
3.8k
Popular Question
to
BioinfGuru
▴ 30
Popular Question
to
Gordon Smyth
50k
Scholar
to
Peter Hickey
▴ 740
Locations
• All
France,
19 minutes ago
United States,
44 minutes ago
WEHI, Melbourne, Australia,
56 minutes ago
Vietnam,
1 hour ago
United States,
1 hour ago
Traffic: 506 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6