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readvcf
•
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0
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0
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488
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
1
vote
12
replies
3.0k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 3.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.2 years ago by
naive
• 0
0
votes
2
replies
1.3k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
3.2 years ago
naive
• 0
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
2
votes
5
replies
2.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
6.8 years ago
Didi
▴ 10
1
vote
4
replies
2.1k
views
cannot allocate memory?
readVcf
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
Haiying.Kong
▴ 110
0
votes
2
replies
1.0k
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf
gt
missing
VariantAnnotation
7.2 years ago
TimothéeFlutre
▴ 80
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
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
0
votes
2
replies
1.6k
views
Duplicated rows in readVcf output
variantannotation
readvcf
updated 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
nicolas.o.rode
• 0
0
votes
1
reply
1.5k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 8.2 years ago by
Julian Gehring
★ 1.3k • written 8.2 years ago by
jolligoodfellow
• 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
1
vote
1
reply
1.1k
views
Suppressing the ID value from writeVcf
readvcf
writevcf
updated 8.5 years ago by
Valerie Obenchain
★ 6.8k • written 8.5 years ago by
fongchunchan
▴ 30
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
2
votes
9
replies
2.7k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
9.0 years ago
askates
▴ 10
0
votes
21
replies
4.3k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
9.0 years ago
pifferdavide
• 0
1
vote
5
replies
4.3k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
9.1 years ago
dan.gatti
• 0
0
votes
2
replies
2.1k
views
Error reading vcf converted from bed file
readvcf
plink
file conversion
bed
bioc-devel
9.1 years ago
mjsduncan
• 0
2
votes
3
replies
2.2k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
9.2 years ago
summerela
• 0
1
vote
12
replies
2.8k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 9.4 years ago by
Valerie Obenchain
★ 6.8k • written 9.4 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
1
reply
1.5k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation
vcf
readvcf
variantannotation
9.4 years ago
jls2282
• 0
2
votes
3
replies
1.3k
views
readVcf skipping CS field in INFO
variantannotation
readVcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
Peter Hickey
▴ 740
0
votes
5
replies
1.7k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
JK
▴ 10
23 results • Page
1 of 1
Recent ...
Replies
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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