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Showing : 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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