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readVcf
•
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0
votes
0
replies
92
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
4 weeks ago
therealgenna
• 0
1
vote
12
replies
1.7k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 23 months ago by
Vincent J. Carey, Jr.
6.6k • written 2.0 years ago by
naive
• 0
0
votes
2
replies
577
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
2.0 years ago
naive
• 0
3
votes
4
replies
1.1k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 4.7 years ago by
Michael Lawrence
11k • written 4.7 years ago by
david.mas
• 0
2
votes
5
replies
2.0k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
5.6 years ago
Didi
▴ 10
1
vote
4
replies
1.6k
views
cannot allocate memory?
readVcf
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
Haiying.Kong
▴ 110
0
votes
2
replies
830
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf
gt
missing
VariantAnnotation
6.1 years ago
TimothéeFlutre
▴ 80
2
votes
4
replies
1.3k
views
Best way to create a VRanges object from a large VCF file?
variantannotation
readvcf
readvcfasvranges
vcf
updated 6.2 years ago by
Michael Lawrence
11k • written 6.2 years ago by
ruben.drews
• 0
0
votes
2
replies
1.2k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R
variantannotation
vcf
scanvcfparam
readvcf
updated 6.8 years ago by
Michael Lawrence
11k • written 6.8 years ago by
emily.mccann
• 0
0
votes
2
replies
1.1k
views
Duplicated rows in readVcf output
variantannotation
readvcf
updated 6.9 years ago by
Valerie Obenchain
★ 6.7k • written 6.9 years ago by
nicolas.o.rode
• 0
0
votes
1
reply
1.2k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 7.0 years ago by
Julian Gehring
★ 1.3k • written 7.0 years ago by
jolligoodfellow
• 0
0
votes
4
replies
2.2k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
7.2 years ago
Marcin Grzybowski
• 0
1
vote
1
reply
875
views
Suppressing the ID value from writeVcf
readvcf
writevcf
updated 7.3 years ago by
Valerie Obenchain
★ 6.7k • written 7.3 years ago by
fongchunchan
▴ 30
2
votes
1
reply
1.1k
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf
vcf
tabix
updated 7.7 years ago by
Valerie Obenchain
★ 6.7k • written 7.7 years ago by
Simon Coetzee
▴ 50
2
votes
9
replies
2.1k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
7.8 years ago
askates
▴ 10
0
votes
21
replies
3.2k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
7.8 years ago
pifferdavide
• 0
1
vote
5
replies
3.6k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
7.9 years ago
dan.gatti
• 0
0
votes
2
replies
1.6k
views
Error reading vcf converted from bed file
readvcf
plink
file conversion
bed
bioc-devel
8.0 years ago
mjsduncan
• 0
2
votes
3
replies
1.7k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
8.1 years ago
summerela
• 0
1
vote
12
replies
2.5k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 8.3 years ago by
Valerie Obenchain
★ 6.7k • written 8.3 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
1
reply
1.3k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation
vcf
readvcf
variantannotation
8.3 years ago
jls2282
• 0
2
votes
3
replies
1.0k
views
readVcf skipping CS field in INFO
variantannotation
readVcf
updated 8.4 years ago by
Valerie Obenchain
★ 6.7k • written 8.4 years ago by
Peter Hickey
▴ 640
0
votes
5
replies
1.4k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 8.4 years ago by
Valerie Obenchain
★ 6.7k • written 8.4 years ago by
JK
▴ 10
23 results • Page
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As an exercise I've tried to analyze simpler but similar experiment. The data is from real experiment (E-MTAB-11224) comparing wild type an…
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Asking for multiple things at once will tend to blow out your results, as you will get every possible combination. ``` > options(timeou…
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by
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Comment: does anyone how to create rarefaction curves from a phyloseq object?
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• 0
I am not sure what you have tried, but the "vegan" library (package) has the ability to do rarefaction. So make sure to load `library("veg…
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