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<prev • 21 results • page 1 of 1 • next >
3
votes
1
answer
175
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1
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Filtering VCFs and Phasing
shapeit vcf filtering vcftools snp written 7 weeks ago by miles.thorburn • 50
2
votes
0
answers
211
views
0
answers
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 3 months ago by moldach • 120
0
votes
1
answer
723
views
1
answer
SHAPEIT error after run: x samples are included in several duos/trios
shapeit inferring haplotypes phasing snp written 17 months ago by c_barbarosie • 0 • updated 4 months ago by chariko • 30
0
votes
0
answers
234
views
0
answers
Benchmarking datasets for Haplotype phasing
genome shapeit haplotype na12891 phasing written 6 months ago by kirannbishwa01 • 930
0
votes
0
answers
243
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0
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extractPIRs is throwing an ERROR
shapeit extractpirs phasing written 10 months ago by nkausthu • 20 • updated 10 months ago by genomax ♦ 62k
1
vote
1
answer
977
views
1
answer
Strand Alignment in ShapeIt -- "Reference and Main panels are not well aligned"
shapeit gwas alignment written 13 months ago by whit18 • 20 • updated 12 months ago by Gennady Khvorykh • 90
0
votes
0
answers
739
views
0
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error when using shapeit2 phasing with vcf from GATK
vcf shapeit phasing written 19 months ago by Loveinheaven • 0 • updated 19 months ago by h.mon ♦ 23k
2
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0
answers
1.1k
views
6 follow
0
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imputation only choose one population as reference panel
shapeit impute2 population gwas written 24 months ago by Peter Chung • 70 • updated 21 months ago by ShirleyDai • 40
2
votes
0
answers
772
views
0
answers
Confused about Effective Population size
shapeit effective population size phasing ne written 24 months ago by andreagarcia871 • 60
0
votes
0
answers
755
views
0
answers
Imputation and phasing of one sample at a time or all samples together ?
shapeit impute2 imputation written 2.1 years ago by ElCascador • 20
0
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0
answers
1.9k
views
0
answers
Haplotype Analysis of Phased Genotype Data
shapeit plink haploview written 2.1 years ago by alakatos • 0
0
votes
0
answers
781
views
0
answers
How do I use haploid variant data to run finestructure or shapeit
shapeit bacteria haploid finestructure written 2.2 years ago by Juliofdiaz • 130
0
votes
0
answers
705
views
0
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result of imputation is vice versa
shapeit imputation minimac3 genotype plink written 2.3 years ago by fatima • 10
0
votes
0
answers
958
views
0
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Segmentation fault error while running extractPIRs from ShapeIT
shapeit vcf bam error segmentation fault written 2.5 years ago by kirannbishwa01 • 930
1
vote
0
answers
1.2k
views
0
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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 2.5 years ago by kirannbishwa01 • 930
1
vote
0
answers
988
views
0
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genotype imputation - alleles
shapeit impute2 imputation written 2.5 years ago by alessandrotestori7 • 330
0
votes
0
answers
735
views
0
answers
Is it possible to get LD statistics keeping haplotype in mind?
shapeit haplotype plink ld r2 written 2.6 years ago by QVINTVS_FABIVS_MAXIMVS • 2.2k
2
votes
1
answer
1.4k
views
1
answer
Haplotype phasing for non-human model organism
shapeit impute2 haplotype phasing beagle written 2.8 years ago by kirannbishwa01 • 930 • updated 2.8 years ago by Zev.Kronenberg ♦ 11k
0
votes
0
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1.3k
views
0
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SHAPEIT allele encoding
shapeit plink phasing written 3.3 years ago by andreagarcia871 • 60
1
vote
0
answers
2.4k
views
0
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SHAPEIT output file confusion
shapeit haplotypes snp written 4.0 years ago by j.a.yearsley • 10
0
votes
1
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2.0k
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1
answer
How to bypass SNPs with identical A1 and A2 alleles in PLINK?
shapeit impute2 merge imputation plink written 4.1 years ago by yorgos.athanasiadis • 40
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