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Where To Get The Genetic Map For The Haplotype Reference Consortium to phase the data externally using SHAPEIT software with family information
genome gwas shapeit phasing hrc written 24 days ago by moldach • 90
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1
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655
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1
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SHAPEIT error after run: x samples are included in several duos/trios
shapeit inferring haplotypes phasing snp written 15 months ago by c_barbarosie • 0 • updated 7 weeks ago by chariko • 30
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172
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Benchmarking datasets for Haplotype phasing
genome shapeit haplotype na12891 phasing written 3 months ago by kirannbishwa01 • 890
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189
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extractPIRs is throwing an ERROR
shapeit extractpirs phasing written 8 months ago by nkausthu • 20 • updated 8 months ago by genomax ♦ 59k
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1
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805
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1
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Strand Alignment in ShapeIt -- "Reference and Main panels are not well aligned"
shapeit gwas alignment written 11 months ago by whit18 • 10 • updated 10 months ago by Gennady Khvorykh • 90
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648
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error when using shapeit2 phasing with vcf from GATK
vcf shapeit phasing written 16 months ago by Loveinheaven • 0 • updated 16 months ago by h.mon ♦ 21k
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1.0k
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6 follow
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imputation only choose one population as reference panel
shapeit impute2 population gwas written 21 months ago by Peter Chung • 70 • updated 19 months ago by ShirleyDai • 40
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713
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Confused about Effective Population size
shapeit effective population size phasing ne written 21 months ago by andreagarcia871 • 60
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695
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Imputation and phasing of one sample at a time or all samples together ?
shapeit impute2 imputation written 22 months ago by ElCascador • 20
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1.7k
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Haplotype Analysis of Phased Genotype Data
shapeit plink haploview written 22 months ago by alakatos • 0
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713
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How do I use haploid variant data to run finestructure or shapeit
shapeit bacteria haploid finestructure written 2.0 years ago by Juliofdiaz • 130
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660
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result of imputation is vice versa
shapeit imputation minimac3 genotype plink written 2.1 years ago by fatima • 10
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891
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Segmentation fault error while running extractPIRs from ShapeIT
shapeit vcf bam error segmentation fault written 2.3 years ago by kirannbishwa01 • 890
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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 2.3 years ago by kirannbishwa01 • 890
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912
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genotype imputation - alleles
shapeit impute2 imputation written 2.3 years ago by alessandrotestori7 • 310
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691
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Is it possible to get LD statistics keeping haplotype in mind?
shapeit haplotype plink ld r2 written 2.4 years ago by QVINTVS_FABIVS_MAXIMVS • 2.2k
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1
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1.3k
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1
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Haplotype phasing for non-human model organism
shapeit impute2 haplotype phasing beagle written 2.6 years ago by kirannbishwa01 • 890 • updated 2.6 years ago by Zev.Kronenberg ♦ 11k
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1.3k
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SHAPEIT allele encoding
shapeit plink phasing written 3.1 years ago by andreagarcia871 • 60
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2.3k
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SHAPEIT output file confusion
shapeit haplotypes snp written 3.8 years ago by j.a.yearsley • 10
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1
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1.9k
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1
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How to bypass SNPs with identical A1 and A2 alleles in PLINK?
shapeit impute2 merge imputation plink written 3.9 years ago by yorgos.athanasiadis • 40
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