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vcf
•
reset
2
votes
2
replies
5.5k
views
how to import/read .vcf files in R
vcf
4.2 years ago
anamarija
▴ 10
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 9.0 years ago by
Valerie Obenchain
★ 6.8k • written 9.0 years ago by
r.jaffe
• 0
4
votes
6
replies
4.1k
views
about collapsed and expanded vcf file
vcf
updated 7.2 years ago by
raggieapauly
• 0 • written 7.2 years ago by
Bogdan
▴ 670
2
votes
3
replies
3.9k
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
3.6k
views
Subset VCF files using multiple criteria
vcf
variantannotation
granges
8.1 years ago
georgewwp
• 0
0
votes
10
replies
2.8k
views
Incorrect row names when a VCF has multiple ALTs.
variantannotation
vcf
updated 9.4 years ago by
Valerie Obenchain
★ 6.8k • written 9.4 years ago by
bicycle1885
• 0
0
votes
4
replies
2.7k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
8.2 years ago
Marcin Grzybowski
• 0
2
votes
9
replies
2.6k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
8.9 years ago • updated 8.8 years ago
askates
▴ 10
2
votes
5
replies
2.5k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
6.7 years ago • updated 6.6 years ago
Didi
▴ 10
1
vote
2
replies
2.5k
views
Any tool to calculate Fst on haploid data?
snps
VCF
updated 22 months ago by
Arafat
• 0 • written 7.1 years ago by
rkdonthu
▴ 10
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
5
replies
2.4k
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
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
5
votes
6
replies
2.2k
views
extracting Allele Read Counts
rsamtools
vcf
7.0 years ago
Bogdan
▴ 670
0
votes
3
replies
2.1k
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
2
votes
4
replies
1.9k
views
Best way to create a VRanges object from a large VCF file?
variantannotation
readvcf
readvcfasvranges
vcf
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
ruben.drews
• 0
0
votes
1
reply
1.8k
views
VCF file non-SNP germline mutations
PureCN
VCF
SNP
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 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
0
replies
1.7k
views
Producing alternate protein sequences from VCF
protein
vcf
8.9 years ago
dan.gatti
• 0
3
votes
8
replies
1.7k
views
problem with @ranges@start in DNAStringSet
vcf
testthat
dnastringset
8.4 years ago
TimothéeFlutre
▴ 80
3
votes
4
replies
1.6k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 5.7 years ago by
Michael Lawrence
★ 11k • written 5.7 years ago by
david.mas
• 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 7.8 years ago by
Michael Lawrence
★ 11k • written 7.8 years ago by
emily.mccann
• 0
1
vote
5
replies
1.6k
views
about filtering variants from a VCF file
vcf
7.2 years ago
Bogdan
▴ 670
0
votes
2
replies
1.5k
views
Error converting vcf to gds
snprelate
vcf
gds
updated 6.0 years ago by
zhengx
▴ 30 • written 6.0 years ago by
annat22
• 0
0
votes
1
reply
1.5k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation
vcf
readvcf
variantannotation
9.3 years ago
jls2282
• 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 5.0 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.0 years ago by
cav3gh
• 0
3
votes
2
replies
1.5k
views
about the use of subsetByFilter()
vcf
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
Bogdan
▴ 670
4
votes
3
replies
1.5k
views
how to save file on local disk after applying predictCoding() function?
vcf
predict coding
save file
VariantAnnotation
updated 9.5 years ago by
Thomas Sandmann
▴ 90 • written 9.5 years ago by
anastasiya-terskih
▴ 10
0
votes
2
replies
1.5k
views
filterVcf: error with param argument
VariantAnnotation
filterVcf
ScanVcfParam
vcf
writeVcf
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
pau.puigdevall
• 0
0
votes
1
reply
1.4k
views
comparing 2 long BED files in R in an efficient way
bed
vcf
updated 5.7 years ago by
GENOMIC_region
• 0 • written 5.7 years ago by
Bogdan
▴ 670
2
votes
1
reply
1.3k
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf
vcf
tabix
updated 8.7 years ago by
Valerie Obenchain
★ 6.8k • written 8.7 years ago by
Simon Coetzee
▴ 50
2
votes
2
replies
1.3k
views
a filter works alone but not with other filters
variantannotation
vcf
filtervcf
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
TimothéeFlutre
▴ 80
0
votes
4
replies
1.3k
views
annotating a vcf file containing Structural Variants
vcf
7.5 years ago
Bogdan
▴ 670
3
votes
2
replies
1.3k
views
VariantAnnotation package, subseting vcfs on fixed fields
variantannotation
vcf
fixed
filter
9.2 years ago
Anna N.
• 0
0
votes
2
replies
1.3k
views
Problem with Annotating Genomic Variant
workflows
vcf
8.8 years ago
merella.stefania
• 0
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
1
reply
1.3k
views
Genome versions of the VcfFiles from AnnotationHub
annotation
software error
vcf
annotationhub
updated 7.9 years ago by
Valerie Obenchain
★ 6.8k • written 7.9 years ago by
sskimb
▴ 10
0
votes
2
replies
1.3k
views
PureCN use of VCF QUAL column for filtering when column is dot
PureCN
VCF
QUAL
updated 5.9 years ago by
markus.riester
▴ 130 • written 5.9 years ago by
twtoal
▴ 10
0
votes
2
replies
1.3k
views
How to correct VCF Iranges from width=1 to correct end coordinate
VCF
iranges
End
software error
variantannotation
9.3 years ago
tiffanie.moss
• 0
0
votes
0
replies
1.2k
views
vcf to venn diagram
snps
vcf
venn diagram
ggplot2
5.3 years ago
mictadlo
▴ 10
1
vote
2
replies
1.2k
views
Expand annotation on a vcf file
vcf
variantannotation
updated 7.7 years ago by
Michael Lawrence
★ 11k • written 7.7 years ago by
Dee
• 0
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
7
votes
3
replies
1.2k
views
Extracting first member of each element of a matrix of lists
variantannotation
vcf
updated 8.9 years ago by
Michael Lawrence
★ 11k • written 8.9 years ago by
Sean Davis
21k
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 8.4 years ago by
TimothéeFlutre
▴ 80
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
5
votes
2
replies
1.1k
views
filter "isSnp" for VCF
variantannotation
filtervcf
vcf
updated 8.4 years ago by
Michael Lawrence
★ 11k • written 8.4 years ago by
TimothéeFlutre
▴ 80
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 4.9 years ago by
maisapinheiro12
• 0
0
votes
1
reply
1.1k
views
Error in matrix
bioconductor
vcf
7.0 years ago
bkauf
• 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
0
votes
3
replies
999
views
rbind VCF Two Objects Column Names Error
VariantAnnotation
VCF
4.8 years ago
Dario Strbenac
★ 1.5k
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
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mercedeh.movassagh
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Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
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This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
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It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
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Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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