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imputation accuracy in beagle
beagle written 4 weeks ago by vinayreddynannuru • 20 • updated 4 weeks ago by zx8754 ♦ 5.4k
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180
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Merge two phased vcf files from 2 pops keeping same ref allele in merged file
bcftools plink beagle written 6 weeks ago by Mr Locuace • 80
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85
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Phasing non-human genomes with Beagle - do I need to divide subjects by population?
snp phasing beagle written 7 weeks ago by mstagliamonte • 0
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1
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140
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1
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ERROR: Missing one or both alleles for a genotype:
vcf gsub impute beagle written 12 weeks ago by vinayreddynannuru • 20 • updated 12 weeks ago by finswimmer ♦ 6.2k
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How to generate the map file for selscan?
selscan phase plink beagle written 3 months ago by Victor • 10
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How to run Beagle to impute missing data using reference panel (1000 genome)?
software impute beagle written 5 months ago by nour.hadjz • 0 • updated 5 months ago by zx8754 ♦ 5.4k
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BEAGLE 4.1 imputation
beagle imputation genotyping written 2.4 years ago by cholingken • 20 • updated 6 months ago by johnnythejota • 0
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393
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Interpreting phased data from Beagle
haplotype imputation genotype phasing beagle written 7 months ago by chadapohn.chaosrikul • 0
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(resolved) BEAGLE 4.1 imputation ending short with "at dag.MergeableDag" message
genome imputation snp beagle written 9 months ago by Ryan O • 0 • updated 8 months ago by RamRS ♦ 18k
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3
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3
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Beagle 4.1 error : Possible data conversion issue
vcf plink snp beagle written 2.9 years ago by aritra90 • 20 • updated 9 months ago by scottf174 • 0
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443
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Problem phasing Indels
indels phasing beagle written 10 months ago by hdtms • 20
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455
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Is there a phasing algorithm or tool that first determines undeniably present haplotypes?
hardy weinberg haplotype phasing beagle written 15 months ago by anp375 • 140
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474
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Beagle Error Reading in .PL file
genome phasing beagle written 15 months ago by karl.fetter • 0
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Beagle Error Code_Unable to access jarfile
sequencing beagle snp error jarfile written 16 months ago by yichen503 • 0 • updated 16 months ago by genomax ♦ 57k
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Convert beagle output file to plink
plink snp beagle written 16 months ago by akang • 90
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904
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Questions about IBD segment detection using beagle
ibd snp beagle written 17 months ago by xgdong912 • 10
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680
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MrBayes Log likelihood stuck on a single value
mrbayes phylogenetics beagle written 21 months ago by Whetting • 1.5k • updated 21 months ago by Biostar ♦♦ 20
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How to determine the haplotypes using Beagle
haplotype snp beagle written 22 months ago by akang • 90
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724
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How to phase my genome from FamilyTreeDNA to haplotypes
hapmap familytreedna snphap phasing beagle written 24 months ago by alexey.minko • 0
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772
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Should variant phasing be performed before or after filtering by Minor Allele Frequency?
maf gwas phasing beagle written 2.2 years ago by i.wilson • 10 • updated 2.1 years ago by Biostar ♦♦ 20
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1.1k
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Can Read Back Phased genotypes be used to extend the haplotype blocks with Beagle, Shapeit, FastPhase etc?
shapeit beagle haplotype fastphase readbackphasing written 2.1 years ago by kirannbishwa01 • 860
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1
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Haplotype phasing for non-human model organism
shapeit impute2 haplotype phasing beagle written 2.5 years ago by kirannbishwa01 • 860 • updated 2.5 years ago by Zev.Kronenberg ♦ 11k
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808
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Is it better to phase two populations together or separately?
populations phasing beagle written 2.9 years ago by eyb • 170 • updated 2.9 years ago by Giovanni M Dall'Olio ♦ 26k
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931
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Phasing a portion of chromosome vs whole chromosome using Beagle?
snp phasing beagle written 3.0 years ago by alek0991 • 0 • updated 2.9 years ago by Biostar ♦♦ 20
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phase genotype data (infer haplotypes) for multiple families
software haplotype family data phasing beagle written 3.2 years ago by Teresa • 0 • updated 3.1 years ago by Biostar ♦♦ 20
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1
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1.5k
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1
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Background information and recommendations for phasing ASW whole genomes
ngs phasing beagle written 4.4 years ago by vlaufer • 250 • updated 3.2 years ago by Biostar ♦♦ 20
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1
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1.3k
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1
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Pre-phasing for imputation BEAGLE or MACH
computing time mach imputation phasing beagle written 3.2 years ago by Laura • 20 • updated 3.2 years ago by nchuang • 180
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Beagle imputation results quality control
vcf imputation beagle written 3.3 years ago by eyb • 170 • updated 3.2 years ago by Biostar ♦♦ 20
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1.6k
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Beagle imputation output, incorrect genotype probability format?
sequence imputation beagle written 3.4 years ago by Tails • 20
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2
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3.7k
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2
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Compare consecutive columns of a file and return the number of non-matching elements
python haplotype beagle written 3.4 years ago by aritra90 • 20 • updated 3.4 years ago by george.ry • 1.1k
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