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318 results • Page
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vcftools
•
reset
1
Vote
10
Replies
431
Views
How to apply vcftools --diff to identify vcf-specific variants/records
vcftools
--diff
--diff-site
21 months ago
Shicheng Guo
♦ 7.5k
• updated 21 months ago
Istvan Albert
87k
0
Votes
0
Replies
106
Views
Linkage disequilibrium from multi-sample vcf file
ld
vcf
snpeff
vcftools
21 months ago
felipead66
• 30
• updated 21 months ago
RamRS
21k
3
Votes
1
Reply
141
Views
Exclude sites on the basis of the proportion of missing data using BCFTOOLS
genome
vcf
vcftools
bcftools
21 months ago
GabrielMontenegro
• 520
2
Votes
3
Replies
189
Views
Replace missing SNPs of one individual with reference alleles in a VCF file
SNP
bcftools
VCFtools
sequencing
21 months ago
amitgourav.ghosh12
• 50
• updated 21 months ago
zx8754
7.5k
33
Votes
9
Replies
9.0k
Views
How To Separate Snp Variants From Indel Variants In The Same Vcf File
vcf
vcftools
9.9 years ago
Jianfengmao
• 310
• updated 21 months ago
rodd
• 40
3
Votes
4
Replies
169
Views
vcftools Warning: Expected at least 2 parts in FORMAT entry
vcftools
21 months ago
Zoey Zou
• 30
1
Vote
0
Replies
122
Views
vcftools counts output not written to file
vcftools
vcf
frequency
counts
SNP
22 months ago
spider_monkey
• 10
1
Vote
6
Replies
1.0k
Views
Updating allele frequency (AF) and minor allele frequency (MAF) INFO fields in .vcf
vcf
vcftools
imputation
QC
SNP
3.0 years ago
JSEM
• 20
• updated 22 months ago
seta
♦ 1.2k
0
Votes
1
Reply
200
Views
Tajima's D equation - VCFtools
tajima
vcftools
22 months ago
bwczech
• 70
0
Votes
4
Replies
246
Views
BCF Tools Filter on 1000Genomes Annotation
bcftools
vcftools
annotation
filter
22 months ago
jon.klonowski
• 10
0
Votes
5
Replies
261
Views
How to turn current VCF into a VCF with genotype and rsID in same file
vcf
bcftools
vcftools
23 months ago
austinkjensen5
• 0
• updated 23 months ago
Kevin Blighe
43k
6
Votes
5
Replies
4.6k
Views
Merge vcf files from Multiple Samples
vcf
vcftools
6.9 years ago
Ron
• 950
• updated 23 months ago
Biostar
20
6
Votes
3
Replies
2.4k
Views
How to add trio information to VCF or PED format (to compute Mendel error in Plink)
plink
vcftools
SNP
4.0 years ago
olavur
• 80
• updated 23 months ago
Biostar
20
0
Votes
0
Replies
222
Views
How to detect outliers from either (a) SNP-Fst or (b) Window-Fst distributions?
Fst
vcftools
23 months ago
serpalma.v
• 20
• updated 23 months ago
h.mon
25k
2
Votes
1
Reply
1.2k
Views
Add rsid to LD output from vcftools
vcf
SNP
LD
vcftools
5.4 years ago
jfertaj
• 90
• updated 23 months ago
zx8754
7.5k
1
Vote
2
Replies
309
Views
Filtering SNPS by minimum LD value in bcftools?
bcftools
vcftools
vcf
LD
r2
23 months ago
RNAseqer
• 110
0
Votes
2
Replies
225
Views
VCFTOOLS won't read my vcf file
snp
vcftools
vcf
23 months ago
wruzic1
• 0
0
Votes
3
Replies
287
Views
Splitting .vcf file
WGS
vcftools
24 months ago
F
♦ 3.4k
0
Votes
5
Replies
698
Views
How to extract proxy SNPs using 1000G vcf for a list of SNPs
plink
proxy
SNP
1000G
vcftools
2.0 years ago
janhuang.cn
• 150
• updated 2.0 years ago
chrchang523
5.2k
12
Votes
3
Replies
24k
Views
Convert VCFf file to plink ped/map format while filtering the SNPs
vcftools
plink
ped
map
6.4 years ago
roll
• 280
• updated 2.0 years ago
hakimeazarafra
• 0
1
Vote
3
Replies
475
Views
Allele frequency visualization
snp
R
stacks
vcftools
2.2 years ago
jaafari.omid
• 40
• updated 2.0 years ago
msimmer92
• 180
4
Votes
14
Replies
370
Views
VCF file filtration
snp
WGS
VCF
bcftools
vcftools
2.1 years ago
jaafari.omid
• 40
0
Votes
1
Reply
498
Views
How vcftools calculate Fst value?
Fst
vcftools
populations
2.1 years ago
seta
♦ 1.2k
0
Votes
1
Reply
1.2k
Views
vcftool negative relatedness values for family members
vcftools
kinship
qc
pedigree
4.7 years ago
marcusanaymik
• 10
• updated 2.1 years ago
Biostar
20
1
Vote
2
Replies
1.0k
Views
"Error: --recode 23 cannot be used with multi-character allele names." when converting VCF to 23andme
vcftools
plink1.9
3.8 years ago
beneficii
• 60
• updated 2.1 years ago
nuria.mauri
• 0
4
Votes
4
Replies
1.9k
Views
How to convert .vcf files into .csv?
vcf
csv
sql
python
vcftools
3.9 years ago
feng9oly
• 0
• updated 2.1 years ago
Biostar
20
5
Votes
7
Replies
1.3k
Views
Extracting certain columns from VCF file
vcf
vcftools
genotype
exome
question
2.8 years ago
gradstudentNew
• 10
• updated 2.2 years ago
zx8754
7.5k
3
Votes
2
Replies
312
Views
Filtering VCFs and Phasing
ShapeIt
VCFtools
filtering
VCF
SNP
2.2 years ago
miles.thorburn
• 80
0
Votes
1
Reply
542
Views
VCFtools calculate SNP density
vcftools
snp density
bioinformatics
vcf
snp
2.2 years ago
christinachavez
• 0
• updated 2.2 years ago
ashishbansal12300
• 0
2
Votes
3
Replies
2.5k
Views
Is the heterozygosity flag (--het) in vcftools calculate observed and expected heterozygosity?
vcftools
vcf
3.6 years ago
ahmedaljumiliy
• 20
• updated 2.2 years ago
Kevin Blighe
43k
1
Vote
7
Replies
2.0k
Views
vcf-subset error: "Wrong number of fields" in vcf file
vcf-subset
vcftools
variant
1000 genomes
vcf
5.5 years ago
Lylthera
• 0
• updated 2.2 years ago
zx8754
7.5k
3
Votes
7
Replies
294
Views
Count variants between two samples within a multi-sample VCF
vcf
VCFTools
2.3 years ago
rc16955
• 60
• updated 2.3 years ago
chrchang523
5.2k
4
Votes
2
Replies
362
Views
split vcf by individual
vcftools
vcf-subset
SNP
vcf
2.3 years ago
sonia.olaechea
• 90
• updated 2.3 years ago
Paul
♦ 1.3k
14
Votes
5
Replies
13k
Views
How to extract sample id using bcftools or vcftools
SNP
vcf
bcftools
vcftools
5.9 years ago
xinhui.wang
• 160
• updated 2.3 years ago
zx8754
7.5k
12
Votes
7
Replies
11k
Views
6 follow
How To Create A Venn Diagram Of Sample1.Vcf, Sample2.Vcf And Sample1&2(Union).Vcf Files
vcftools
mpileup
9.1 years ago
Deniz
• 50
• updated 2.3 years ago
zx8754
7.5k
2
Votes
3
Replies
1.3k
Views
Split a large VCF into user defined regions
sequencing
vcf
vcftools
4.4 years ago
zelia.worman
• 0
• updated 2.3 years ago
zx8754
7.5k
7
Votes
7
Replies
5.9k
Views
Most effective way to merge individual VCF files into VCF files merged by chromosome
VCF
VCFmerge
VCFtools
merge
Plinkseq
6.8 years ago
vlaufer
• 260
• updated 2.3 years ago
Biostar
20
2
Votes
5
Replies
831
Views
vcftools --TajimaD in sliding windows
vcftools
SNP
Tajima's D
2.3 years ago
sonia.olaechea
• 90
12
Votes
2
Replies
951
Views
Tutorial:
Fast LD computation from VCF files using tomahawk
vcf
vcftools
bcftools
ld
snp
Tutorial
2.3 years ago
rmf
• 630
4
Votes
5
Replies
498
Views
How do I use vcftools to filter by variant ID OR variant position?
vcftools
2.3 years ago
jwhite007
• 10
• updated 2.3 years ago
Pierre Lindenbaum
120k
0
Votes
4
Replies
282
Views
NCBI Remap Issue
remapping
vcftools
GWAS
genome
SNP
2.4 years ago
f.abbondanza94
• 0
1
Vote
7
Replies
841
Views
vcftools Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.
vcftools
vcf
2.4 years ago
mayara.salvian
• 10
• updated 2.4 years ago
Pierre Lindenbaum
120k
1
Vote
11
Replies
457
Views
vcftools vcf-merge error
vcftools
vcf-merge
2.4 years ago
biogirl
• 170
3
Votes
2
Replies
926
Views
VCFtools version for LD calculations specifying bin size
vcftools
LD
2.5 years ago
Stephanie
• 30
• updated 2.5 years ago
Kevin Blighe
43k
1
Vote
2
Replies
1.4k
Views
using vcftools to add gene name to vcf file
vcftools
5.0 years ago
bioguy24
• 190
• updated 2.5 years ago
RamRS
21k
1
Vote
2
Replies
1.3k
Views
add gene name from bed file to vcf in vcftools
vcftools
5.0 years ago
bioguy24
• 190
• updated 2.5 years ago
RamRS
21k
1
Vote
3
Replies
576
Views
bcftools: DP filter based on chromosome and sex
bcftools
wgs
samtools
vcftools
pyvcf
2.5 years ago
bsmith030465
• 140
• updated 2.5 years ago
Pierre Lindenbaum
120k
0
Votes
4
Replies
353
Views
Merging variant replicates rather than filtering
GWAS
Plink
vcftools
2.5 years ago
dylkot
• 0
• updated 2.5 years ago
chrchang523
5.2k
7
Votes
14
Replies
5.8k
Views
9 follow
Filtering Imputation output: how to filter on a VCF INFO field
imputation
filtering
minimac3
plink
vcftools
4.6 years ago
mmagoo6
• 50
• updated 2.5 years ago
natalia.han
• 0
5
Votes
4
Replies
655
Views
VCFtools. Get rid of DS:GP phased genotypes while keeping GT and remaining fields
VCFtools
2.6 years ago
Mr Locuace
• 90
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