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readvcf
•
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0
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0
replies
825
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
2.2 years ago
therealgenna
• 0
1
vote
12
replies
4.3k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 4.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 4.2 years ago by
naive
• 0
0
votes
2
replies
1.9k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
4.2 years ago
naive
• 0
3
votes
4
replies
2.2k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 6.9 years ago by
Michael Lawrence
★ 11k • written 6.9 years ago by
david.mas
• 0
2
votes
5
replies
3.1k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
7.8 years ago
Didi
▴ 10
1
vote
4
replies
2.6k
views
cannot allocate memory?
readVcf
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
Haiying.Kong
▴ 110
0
votes
2
replies
1.3k
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf
gt
missing
VariantAnnotation
8.2 years ago
TimothéeFlutre
▴ 80
2
votes
4
replies
2.5k
views
Best way to create a VRanges object from a large VCF file?
variantannotation
readvcf
readvcfasvranges
vcf
updated 8.3 years ago by
Michael Lawrence
★ 11k • written 8.3 years ago by
ruben.drews
• 0
0
votes
2
replies
2.0k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R
variantannotation
vcf
scanvcfparam
readvcf
updated 8.9 years ago by
Michael Lawrence
★ 11k • written 8.9 years ago by
emily.mccann
• 0
0
votes
2
replies
1.9k
views
Duplicated rows in readVcf output
variantannotation
readvcf
updated 9.1 years ago by
Valerie Obenchain
★ 6.8k • written 9.1 years ago by
nicolas.o.rode
• 0
0
votes
2
replies
2.0k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 7 months ago by
Danyiel
• 0 • written 9.2 years ago by
jolligoodfellow
• 0
0
votes
4
replies
3.1k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
9.4 years ago
Marcin Grzybowski
• 0
1
vote
1
reply
1.3k
views
Suppressing the ID value from writeVcf
readvcf
writevcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
fongchunchan
▴ 30
2
votes
1
reply
1.8k
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf
vcf
tabix
updated 9.8 years ago by
Valerie Obenchain
★ 6.8k • written 9.8 years ago by
Simon Coetzee
▴ 50
2
votes
9
replies
3.4k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
10.0 years ago
askates
▴ 10
0
votes
21
replies
5.3k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
10.0 years ago
pifferdavide
• 0
1
vote
5
replies
4.9k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
10.1 years ago
dan.gatti
• 0
0
votes
2
replies
2.5k
views
Error reading vcf converted from bed file
readvcf
plink
file conversion
bed
bioc-devel
10.1 years ago
mjsduncan
• 0
2
votes
3
replies
2.8k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
10.2 years ago
summerela
• 0
1
vote
12
replies
3.2k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 10.4 years ago by
Valerie Obenchain
★ 6.8k • written 10.4 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
1
reply
1.7k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation
vcf
readvcf
variantannotation
10.4 years ago
jls2282
• 0
2
votes
3
replies
1.5k
views
readVcf skipping CS field in INFO
variantannotation
readVcf
updated 10.5 years ago by
Valerie Obenchain
★ 6.8k • written 10.5 years ago by
Peter Hickey
▴ 750
0
votes
5
replies
2.0k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 10.5 years ago by
Valerie Obenchain
★ 6.8k • written 10.5 years ago by
JK
▴ 10
23 results • Page
1 of 1
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Replies
Answer: GSVA 1.52.2 (new API) nb of workers?
by
chaneymiller5908958
• 0
@[block blast][1] I'm running into the same issue with the parallelization. [1]: https://blockblastonline.com
Comment: Setting ylims in bam coverage plot and assigning compound sashimi numbers to ove
by
macdonaldfrench7286566
• 0
Regarding the ylim for the coverage [space waves][1], have you tried accessing the ylim slot of the CoverageTrack object after you've creat…
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an
by
Kateřina
• 0
I unfortunately haven't. Non-tidy grammar is fine, but I have wanted to use tidy-only grammar. Thank you nonetheless!
Comment: GAlignments Cigar to GRanges
by
pineiroalejandro
• 0
Wow, so easy! Thanks for your quick reply.
Comment: EuroBioC2023 abstract submission is open!
by
eilishhill8
• 0
Thanks for sharing this. I got it clearly now. Submit here: [https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/][1] [melon sa…
Votes
Answer: GAlignments Cigar to GRanges
Answer: GAlignments Cigar to GRanges
When running contrasts, does it use normalized read counts?
When running contrasts, does it use normalized read counts?
Importing Salmon counts with tximport with host and virus genomes
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