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4
votes
3
replies
664
views
where to find GRCh38 for 1000 Genomes
VCF GRCh38 1000Genomes
updated 17 months ago by 10k • written 18 months ago by ▴ 100
9
votes
6
replies
1.9k
views
where can i find the GRCh38 genetic map for IMPUTE2
map GRCh38 IMPUTE2
18 months ago by raalsuwaidi ▴ 100
0
votes
0
replies
227
views
How does IMPUTE2 calculate concordance
concordance IMPUTE2
19 months ago by raalsuwaidi ▴ 100
2
votes
3
replies
552
views
How to perform imputation analysis between masked SNPs and ground truth
GWAS SNPs IMPUTE2
updated 19 months ago by 3.7k • written 19 months ago by ▴ 100
0
votes
0
replies
287
views
How to calculate r2 for IMPUTE2
r2 IMPUTE2
19 months ago by raalsuwaidi ▴ 100
6
votes
6
replies
912
views
how to remove positions in VCF based on rsID
vcf plink bcftools
updated 3 months ago by 40k • written 19 months ago by ▴ 100
0
votes
0
replies
266
views
How does IMPUTE2 assigns snp_id
SNP VCF IMPUTE2 bcftools PLINK
19 months ago by raalsuwaidi ▴ 100
3
votes
1
reply
1.1k
views
how to convert from hap/legend to VCF
-merge_ref_panels_output_ref VCF IMPUTE2
updated 20 months ago by 10k • written 20 months ago by ▴ 100
1
vote
4
replies
889
views
how to loop and select values from a python dataframe
dataframe python
20 months ago by raalsuwaidi ▴ 100
2
votes
1
reply
663
views
understand and how to plot the PLINK mdist file
plink mdist plot
20 months ago by raalsuwaidi ▴ 100
0
votes
2
replies
845
views
help with CrossMap
VCF hg38 hg19 CrossMap
19 months ago by raalsuwaidi ▴ 100
6
votes
2
replies
2.1k
views
struggling in using bcftools to set variants to missing
missing2ref setGT bcftools vcf
updated 7 months ago by • 0 • written 22 months ago by ▴ 100
0
votes
0
replies
333
views
map files
genome impute2 map
23 months ago by raalsuwaidi ▴ 100
0
votes
0
replies
343
views
IMPUTE2 -merge_ref_panels output
IMPUTE2
23 months ago by raalsuwaidi ▴ 100
0
votes
0
replies
413
views
Distance matrix PCA
HAP PCA distance
23 months ago by raalsuwaidi ▴ 100
3
votes
9
replies
1.7k
views
IMPUTE2 -merge_ref_panels
IMPUTE2 -merge_ref_panels
updated 2.0 years ago by 86k • written 2.0 years ago by ▴ 100
1
vote
2
replies
583
views
custom reference panel
sample impute GWAS
2.0 years ago by raalsuwaidi ▴ 100
3
votes
4
replies
1.7k
views
color coded PCA plot in R for a combined set
plink pca plot
2.2 years ago by raalsuwaidi ▴ 100
3
votes
4
replies
1.1k
views
PCA for combined set
plink bcftools vcf PCA
2.2 years ago by raalsuwaidi ▴ 100
1
vote
2
replies
528
views
Combining two vcf files
Vcf GWAS
2.2 years ago by raalsuwaidi ▴ 100
0
votes
0
replies
524
views
Combining data sets for PCA
Plink 1000genome PCA genotype
2.2 years ago by raalsuwaidi ▴ 100
4
votes
4
replies
1.1k
views
setting genotypes to missing
genotype vcf impute
2.3 years ago by raalsuwaidi ▴ 100
1
vote
2
replies
852
views
missing REF and ALT in vcf
REF SNP VCF ALT
2.3 years ago by raalsuwaidi ▴ 100
4
votes
7
replies
1.4k
views
Mask a SNP before imputation
genotype bcftools impute2 mask VCF
2.0 years ago by raalsuwaidi ▴ 100
1
vote
1
reply
683
views
two allele frequency
allele position BCFTOOLS
updated 2.4 years ago by 14k • written 2.4 years ago by ▴ 100
0
votes
0
replies
468
views
error when imputing for mismatch legend file
impute2 haps shapeit legend
2.5 years ago by raalsuwaidi ▴ 100
0
votes
2
replies
1.0k
views
VCF rare variants and exon
vcf exon rare variants
3.5 years ago by raalsuwaidi ▴ 100
0
votes
3
replies
1.1k
views
IMPUTE2 variable question
vcf impute2 imputation
updated 3.5 years ago by 86k • written 3.5 years ago by ▴ 100
7
votes
5
replies
923
views
what does ./1 in a VCF file means
vcf genome snp sequence
updated 3.5 years ago by ▴ 950 • written 3.5 years ago by ▴ 100
29 results • Page 1 of 1
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