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VCF
•
reset
0
votes
0
replies
499
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
15 months ago
therealgenna
• 0
0
votes
0
replies
511
views
Prepare data frame of 3 column-lists or matrix of three-column lists from VCF or BAM files
BAM
Segmentation
CINdex
VCF
Data
21 months ago
raven1306
• 0
1
vote
2
replies
2.6k
views
Any tool to calculate Fst on haploid data?
snps
VCF
updated 2.0 years ago by
Arafat
• 0 • written 7.2 years ago by
rkdonthu
▴ 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
Martin Morgan
25k • written 4.1 years ago by
W. van Rengs
• 0
2
votes
2
replies
5.8k
views
how to import/read .vcf files in R
vcf
4.3 years ago
anamarija
▴ 10
0
votes
1
reply
806
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
4.9 years ago
Elena.M
• 0
0
votes
3
replies
1.0k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation
VCF
5.0 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
Julian Gehring
★ 1.3k • written 5.0 years ago by
maisapinheiro12
• 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
Stephanie M. Gogarten
▴ 870 • written 5.1 years ago by
cav3gh
• 0
0
votes
1
reply
1.0k
views
Bioconductor and WGS: recommended practices?
whole genome sequencing
variants
vcf
WGS
5.3 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 5.9 years ago by
Michael Lawrence
★ 11k • written 5.9 years ago by
david.mas
• 0
0
votes
1
reply
1.5k
views
comparing 2 long BED files in R in an efficient way
bed
vcf
updated 5.9 years ago by
GENOMIC_region
• 0 • written 5.9 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 5.9 years ago by
Valerie Obenchain
★ 6.8k • written 5.9 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 6.1 years ago by
markus.riester
▴ 130 • written 6.1 years ago by
twtoal
▴ 10
0
votes
2
replies
1.6k
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
6.8 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
Martin Morgan
25k • written 7.1 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
2.5k
views
merge vcf files with different samples and variants?
vcf
written 7.2 years ago by
shilin.zhao
▴ 40
4
votes
6
replies
4.2k
views
about collapsed and expanded vcf file
vcf
updated 7.3 years ago by
raggieapauly
• 0 • written 7.4 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 7.4 years ago by
ruben.drews
• 0
3
votes
2
replies
1.5k
views
about the use of subsetByFilter()
vcf
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
Bogdan
▴ 670
1
vote
5
replies
1.6k
views
about filtering variants from a VCF file
vcf
7.4 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
Valerie Obenchain
★ 6.8k • written 7.4 years ago by
Sean Davis
21k
0
votes
1
reply
1.2k
views
vcfR package vector length error
vcf
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
jenniewoo
▴ 70
0
votes
4
replies
1.4k
views
annotating a vcf file containing Structural Variants
vcf
7.7 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
Michael Lawrence
★ 11k • written 7.8 years ago by
Andy Lynch
▴ 120
1
vote
2
replies
1.3k
views
Expand annotation on a vcf file
vcf
variantannotation
updated 7.9 years ago by
Michael Lawrence
★ 11k • written 7.9 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 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
sskimb
▴ 10
0
votes
1
reply
3.7k
views
Subset VCF files using multiple criteria
vcf
variantannotation
granges
8.3 years ago
georgewwp
• 0
0
votes
3
replies
2.2k
views
vcf postion extract
vcf
variantannotation
position
updated 8.3 years ago by
Martin Morgan
25k • written 8.3 years ago by
1000G_Q
• 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
2.6k
views
Plot data from VCF using Gviz?
gviz
variantannotation
vcf
updated 8.5 years ago by
Valerie Obenchain
★ 6.8k • written 8.5 years ago by
Johannes Rainer
★ 2.0k
2
votes
3
replies
1.2k
views
genotypeToSnpMatrix doesn't handle PL
variantannotation
vcf
updated 8.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 8.6 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
1.4k
views
a filter works alone but not with other filters
variantannotation
vcf
filtervcf
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
TimothéeFlutre
▴ 80
5
votes
2
replies
1.1k
views
filter "isSnp" for VCF
variantannotation
filtervcf
vcf
updated 8.6 years ago by
Michael Lawrence
★ 11k • written 8.6 years ago by
TimothéeFlutre
▴ 80
0
votes
2
replies
1.5k
views
filterVcf: error with param argument
VariantAnnotation
filterVcf
ScanVcfParam
vcf
writeVcf
updated 8.8 years ago by
Martin Morgan
25k • written 8.8 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
8.9 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
Michael Lawrence
★ 11k • written 9.1 years ago by
Sean Davis
21k
0
votes
0
replies
1.7k
views
Producing alternate protein sequences from VCF
protein
vcf
9.1 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 9.2 years ago by
Valerie Obenchain
★ 6.8k • written 9.2 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
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
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• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
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Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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