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How to decide method for imputing the missing genotype in a VCF
shapeit impute2 imputation beagle written 16 days ago by nchuang • 200
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169
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Is it acceptable to use ShapeIT for parasite genomes?
shapeit impute2 haplotype phasing beagle written 3 months ago by nataliagru1 • 30 • updated 7 weeks ago by Biostar ♦♦ 20
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165
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Recombination maps for cattle
genome impute2 snp assembly written 7 weeks ago by mdyogolos • 10
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1
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259
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1
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IMPUTE2- Map file for custom reference panel
impute2 reference panel imputation written 5 months ago by john.michel.rouhana • 10 • updated 5 months ago by h.mon ♦ 28k
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2
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2.1k
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Convert IMPUTE2 to VCF while keeping phase information
vcf impute2 phasing conversion written 4.0 years ago by lkmklsmn • 890 • updated 6 months ago by croshong75 • 0
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1
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478
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1
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How to get imputation accuracy/quality after using IMPUTE2?
impute2 impute statistics written 8 months ago by Wan Shi Tong • 60
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645
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Low SNP imputation concordance - except chromosome 1
impute2 imputation plink snp gwas written 15 months ago by muraved • 10
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1
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663
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1
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How calculate MAF from impute2 output in R
maf impute2 snp written 17 months ago by vgenepi • 10 • updated 15 months ago by zx8754 ♦ 8.4k
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2
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1.1k
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From Impute2 to PLINK: when to merge chromosome files?
impute2 imputation plink gwas written 22 months ago by whit18 • 20 • updated 22 months ago by Wietje • 210
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Impute2 Custom Reference Panel
impute2 imputation reference recombination map written 4.0 years ago by ngsgene • 350 • updated 23 months ago by Kevin Blighe ♦ 51k
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738
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Help Please! Stuck in .bed format and need to convert for Impute2
impute2 liftover written 24 months ago by whit18 • 20
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784
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Problem imputing (large) file into GenABEL
impute2databel impute2 genabel written 2.1 years ago by m93 • 170
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708
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IMPUTE2: change names of specific SNPs
impute2 snps names written 2.2 years ago by m93 • 170
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is it .impute2 format equal to .gen format
impute2 imputation qctool written 2.4 years ago by Peter Chung • 80 • updated 2.2 years ago by Biostar ♦♦ 20
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6 follow
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imputation only choose one population as reference panel
shapeit impute2 population gwas written 2.7 years ago by Peter Chung • 80 • updated 2.5 years ago by ShirleyDai • 40
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1.4k
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Improving accuracy in small regions with Impute2
genome imputation accuracy snp impute2 written 4.5 years ago by lel7lel7 • 30 • updated 2.7 years ago by Biostar ♦♦ 20
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Imputation and phasing of one sample at a time or all samples together ?
shapeit impute2 imputation written 2.8 years ago by ElCascador • 20
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Imputation 1000 Genome and plink file
imputation 1000 genome impute2 written 2.9 years ago by mzezza • 10
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3
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7 follow
3
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How to convert IMPUTE2 to VCF format
vcf impute2 conversion written 4.3 years ago by lkmklsmn • 890 • updated 3.0 years ago by dweeks.pitt • 40
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1.2k
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genotype imputation - alleles
shapeit impute2 imputation written 3.2 years ago by alessandrotestori7 • 350
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IMPUTE2 reference allele: same as matrixEQTL?
matrixeqtl impute2 imputation snp written 3.4 years ago by User 7754 • 230
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986
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IMPUTE2 data extraction
impute2 data extraction written 3.5 years ago by tushardave26 • 10
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1
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1.6k
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1
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Haplotype phasing for non-human model organism
shapeit impute2 haplotype phasing beagle written 3.5 years ago by kirannbishwa01 • 1.1k • updated 3.5 years ago by Zev.Kronenberg ♦ 11k
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1.5k
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Imputing specific SNPs and merging with original dataset
impute2 imputation plink snp gwas written 3.6 years ago by mbxtp1 • 0
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1.4k
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Subset dosage data
dosage impute2 plink gwas written 3.7 years ago by Veera • 90
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Subsetting individuals from IMPUTE2 ref files: .hap and .legend
genome impute2 written 3.8 years ago by GabrielMontenegro • 540
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1
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3.4k
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6 follow
1
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Which reference panel to use with Impute2
impute2 format 1000 genome written 5.2 years ago by raja.venks • 20 • updated 3.9 years ago by tulsi1192 • 0
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1
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2.9k
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1
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How to convert vcf to impute2 format?
vcf impute2 conversion written 4.1 years ago by grishin • 10
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1.5k
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1
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Loading IMPUTE2 dosage data into plink/seq
dosage plink/seq impute2 written 4.4 years ago by potassiumiodide0990 • 80 • updated 4.3 years ago by Vincent Laufer • 1.1k
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1
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.map file for Impute2
convert file format .map plink impute2 written 4.3 years ago by lmh327 • 0 • updated 4.3 years ago by chrchang523 ♦ 5.8k
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