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Showing top results for tag:
plink
•
reset
0
votes
0
replies
93
views
GWAS from direct samples... is imputation necessary?
imputation
PLINK
GWAS
1 day ago by
sabrilo171
▴ 10
3
votes
3
replies
208
views
IDAT to FASTA workflow
PLINK
R
IDAT
FASTA
GWAS
updated 1 day ago by
GenoMax
146k • written 1 day ago by
sabrilo171
▴ 10
1
vote
1
reply
241
views
1000 genome dataset download
ADMIXTURE
1000genome
iAdmix
fastNGSadmix
plink
updated 10 days ago by
chrchang523
11k • written 11 days ago by
Soohyun
• 0
106
votes
109
replies
52k
views
29 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 12 days ago by
LChart
4.3k • written 6.2 years ago by
Kevin Blighe
88k
0
votes
0
replies
178
views
Setting up a case control with 18 VCFs in plink?
case-control
plink
WGS
21 days ago by
atopasn1
• 0
0
votes
2
replies
289
views
Merging bfiles
fam
plink
bfile
bed
18 days ago by
aj123
▴ 120
3
votes
3
replies
365
views
Pedigree information
pedigree
plink
king
updated 4 weeks ago by
bk11
★ 3.0k • written 4 weeks ago by
heureuse
• 0
0
votes
0
replies
155
views
How to calculate inbreeding coefficient out of ROH (Plink)
plink
5 weeks ago by
t-ishige
• 0
0
votes
1
reply
293
views
Plink HWE QC question
HWE
Plink
p-value
updated 6 weeks ago by
bk11
★ 3.0k • written 6 weeks ago by
janny.lau
▴ 10
3
votes
3
replies
433
views
Ancestry estimation using 1000 genomes as reference
ancestry
plink
1000genomes
updated 8 weeks ago by
Jeremy Leipzig
22k • written 8 weeks ago by
kasgel
• 0
2
votes
1
reply
321
views
Updating phenotype column for .ped .fam files (PLINK --pheno not working)
phenotype
PLINK
--pheno
GWAS
binary
updated 9 weeks ago by
bk11
★ 3.0k • written 9 weeks ago by
sabrilo171
▴ 10
4
votes
5
replies
621
views
LD Pruning in GWAS
PLINK
PCA
pruning
LD
GWAS
updated 9 weeks ago by
LauferVA
4.5k • written 9 weeks ago by
Smriti
▴ 30
1
vote
1
reply
429
views
How to deal with warnings from PLINK while performing QC using HAPMAP data ?
QC
Hapmap
PLINK
GWAS
updated 9 weeks ago by
Kevin Blighe
88k • written 11 weeks ago by
Yugan Gogul Muthukumar
▴ 10
0
votes
2
replies
860
views
Apply Plink2 Score - Error Invalid chromosome code
plink
plink2
pgsc_calc
plink2score
updated 9 weeks ago by
Ruijiang HAN
▴ 10 • written 15 months ago by
h171linux
• 0
0
votes
4
replies
543
views
PLINK error doing a GWAS
phenotype
PLINK
covariates
association
GWAS
updated 9 weeks ago by
chrchang523
11k • written 10 weeks ago by
david.badenas.01
• 0
1
vote
6
replies
585
views
Analyzing PCA Clustering from PLINK Output
plink
9 weeks ago by
Smriti
▴ 30
0
votes
0
replies
165
views
Generate the snpfile.txt (for BLUPF90 input) in 0125 format from plink flat file (.map and .ped)?
Genotype
BLUPF90
PLINK
updated 10 weeks ago by
GenoMax
146k • written 10 weeks ago by
tvibhaps
▴ 10
0
votes
5
replies
661
views
Segmentation fault PLINK 1.90b
PLINK
updated 10 weeks ago by
chrchang523
11k • written 11 weeks ago by
Alexandros.Frydas
▴ 30
0
votes
0
replies
183
views
BCftools call when using -v -V indels vs using -V indels only
BCftools
plink
10 weeks ago by
Jimmy M
• 0
1
vote
1
reply
306
views
Can i use population as a trait to perform GWAS?
Hapmap
PLINK
GWAS
QC
updated 10 weeks ago by
dthorbur
★ 2.5k • written 11 weeks ago by
Yugan Gogul Muthukumar
▴ 10
1
vote
2
replies
351
views
How to fix this error while performing QC in PLINK "Warning: 228 het. haploid genotypes present"
Hapmap
PLINK
GWAS
QC
11 weeks ago by
Yugan Gogul Muthukumar
▴ 10
0
votes
0
replies
237
views
Convert Illumina Final Report.txt file into PLINK input files (.fam, .lgen, .ped etc)
PLINK
12 weeks ago by
Alexandros.Frydas
▴ 30
0
votes
1
reply
274
views
PCA Genotyping rate 1000genome and own data
quality
genotypingrate
pca
plink
genomics
updated 3 months ago by
LChart
4.3k • written 3 months ago by
curious_butterfly
• 0
0
votes
0
replies
208
views
Does Plink under perform ? ( GWAS )
snp
gwas
qq-plot
plink
updated 3 months ago by
GenoMax
146k • written 3 months ago by
basnet.soren
• 0
0
votes
1
reply
317
views
Multi allelic variants extraction with plink
plink
multiallelic-variants
updated 3 months ago by
chrchang523
11k • written 3 months ago by
_quantum_girl_
▴ 60
5
votes
12
replies
4.6k
views
10 follow
ADMIXTURE Segmentatio fault
admixture
plink
vcf
updated 3 months ago by
Etienne DVRK
• 0 • written 3.4 years ago by
pmc.sa
▴ 40
0
votes
0
replies
244
views
How to best check allele flipping between bed files?
plink
bed
3 months ago by
DN99
▴ 20
3
votes
3
replies
628
views
LD SNP pruning with plink
LD-pruning
plink
3 months ago by
celia
▴ 10
0
votes
0
replies
240
views
mismatch allele problem PLINK
PLINK
updated 3 months ago by
Ram
44k • written 3 months ago by
luca.sclisizzo
• 0
1
vote
1
reply
284
views
Discrepancies in F Coefficient and Heterozygosity Estimates
population-genetics
F-coefficient
plink
vcftools
updated 3 months ago by
Ram
44k • written 3 months ago by
eleftosi
• 0
3
votes
5
replies
730
views
ROH and Manhattan plot
ROH
Manhattan
plink
updated 4 months ago by
bk11
★ 3.0k • written 4 months ago by
Star:)
▴ 50
0
votes
8
replies
1.1k
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 4 months ago by
Ram
44k • written 5 months ago by
ajbarrett98
• 0
0
votes
0
replies
311
views
I need to binary plink files of human genome reference build37, however, Im completely lost and have no idea from where to begin
bplinkfiles
human
genome
plink
updated 4 months ago by
GenoMax
146k • written 4 months ago by
Marcos
• 0
1
vote
2
replies
445
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
5 months ago by
F110152169
• 0
1
vote
2
replies
881
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 5 months ago by
Muhammad
• 0 • written 3.0 years ago by
mari.lynne
• 0
1
vote
5
replies
654
views
Annotating file using bcftools
annotation
plink
bcftools
5 months ago by
kl
▴ 10
0
votes
1
reply
349
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 5 months ago by
chrchang523
11k • written 5 months ago by
analyst
▴ 50
0
votes
0
replies
252
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
5 months ago by
Samantha
• 0
0
votes
0
replies
209
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 5 months ago by
Ram
44k • written 5 months ago by
curious_butterfly
• 0
4
votes
1
reply
412
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 5 months ago by
zx8754
12k • written 6 months ago by
Jautis
▴ 580
0
votes
5
replies
765
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 6 months ago by
chrchang523
11k • written 6 months ago by
curious
▴ 810
1
vote
0
replies
264
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 5 months ago by
zx8754
12k • written 6 months ago by
Emilie
▴ 10
8
votes
16
replies
2.0k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 6 months ago by
bk11
★ 3.0k • written 7 months ago by
Sofia
• 0
1
vote
3
replies
2.7k
views
Problem to remove subset of patients with plink
plink
PED
updated 6 months ago by
chrchang523
11k • written 6.6 years ago by
Ginevra
▴ 10
1
vote
1
reply
606
views
Plink merge errors.
cygwin64
bed
PLINK
6 months ago by
Dinmukhamed
• 0
0
votes
0
replies
300
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 6 months ago by
Ram
44k • written 6 months ago by
Dinmukhamed
• 0
0
votes
0
replies
340
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
6 months ago by
enferdeflame
• 0
0
votes
0
replies
270
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 6 months ago by
GenoMax
146k • written 6 months ago by
srimmer
• 0
0
votes
2
replies
484
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
6 months ago by
Koketso
• 0
4
votes
4
replies
1.1k
views
How do I install plink2 on a mac?
plink2
plink
updated 6 months ago by
zx8754
12k • written 6 months ago by
emilija.romic
▴ 10
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