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How does beagle get phase for sites that are NOT in the reference panel
imputation phasing beagle written 1 day ago by curious • 430
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Bacterial population reconstruction
haplotype population phase phasing written 8 weeks ago by SemiQuant • 70
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Phases switches in local ancestry inference (LAMP-LD vs RFMix)
rfmix phase switches phasing lamp-ld written 4 months ago by Mr Locuace • 100
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Phasing with Beagle
haplotypes phasing beagle written 4 months ago by gabri.mochales • 30
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Transferring Phase information from one VCF to another
vcf phasing written 6 months ago by ma17 • 10 • updated 6 months ago by WouterDeCoster ♦ 44k
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Forum: Phasing with Falcon
assembly phasing tutorial falcon phase forum written 6 months ago by Juke34 • 4.6k
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Is it acceptable to use ShapeIT for parasite genomes?
shapeit impute2 haplotype phasing beagle written 13 months ago by nataliagru1 • 50 • updated 6 months ago by Biostar ♦♦ 20
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Shapeit2 cannot open reference panel
gwas phasing shapeit2 written 7 months ago by sunnysean • 20 • updated 7 months ago by Kevin Blighe ♦ 65k
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Genetic map for chromosome X that shows recombination rates?
shapeit phasing written 7 months ago by curious • 430 • updated 7 months ago by Kevin Blighe ♦ 65k
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Trouble understanding Eagle2 phasing software "--allowRefAltSwap" flag
eagle phasing written 7 months ago by curious • 430
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Evaluating switch error rate when phasing with Eagle2?
eagle gwas phasing beagle written 7 months ago by curious • 430
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When using Eagle, is the X chromosome typically phased without including pseudoautosomal regions?
eagle phasing written 8 months ago by curious • 430
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189
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Hapblock from snp file
vcf snp haplotype haplogroup phasing written 8 months ago by devarora • 230
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How to phase my own 23andMe data ?
23andme phasing snp written 10 months ago by LouisJoubert • 10 • updated 10 months ago by Charles Warden ♦ 7.8k
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Problems installing shapeit
shapeit phasing written 10 months ago by michael.flower.14 • 0
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transmitted and untransmitted alleles
hapmap haplotype snp phasing written 10 months ago by yh362 • 30 • updated 10 months ago by Kevin Blighe ♦ 65k
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hapcut2 output and figures
hapcut2 phasing written 12 months ago by rob234king • 600
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Parent of Origin analysis in trio dataset
trio parent of origin vcftoos phasing premim written 14 months ago by a.zore2 • 10 • updated 13 months ago by Biostar ♦♦ 20
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BEAGLE 4.0 with ped file output into Refined IBD not identifying segments properly
software error pedigree refined ibd phasing beagle written 14 months ago by LTDavid • 20
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refine population phased haplotypes by pedigree
pedigree population genotype phasing written 18 months ago by samuelandjw • 20 • updated 13 months ago by bmstudent • 0
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Merge phased files from ShapeIT
shapeit phasing written 14 months ago by nataliagru1 • 50 • updated 14 months ago by Charles Warden ♦ 7.8k
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Running beagle 5.0 Refined-IBD with no map file gives an empty output
refined-ibd phasing beagle written 15 months ago by wz • 0
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Genotype phasing with lack of parental information - compound heterozygous
trio genotype phasing sequencing written 15 months ago by vntt2407 • 10
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308
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mutation phasing of a family data
exome family phasing snp written 17 months ago by sagardesai91 • 50 • updated 15 months ago by Biostar ♦♦ 20
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529
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SHAPEIT - getting 'Segmentation fault'
shapeit haplotyping haplotype phasing written 16 months ago by Larson • 0
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searching tool for calculating switch/phase error rate
vcf variants phasing whatshap written 18 months ago by WouterDeCoster ♦ 44k • updated 16 months ago by cruzpedro • 60
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Convert IMPUTE2 to VCF while keeping phase information
vcf impute2 phasing conversion written 4.8 years ago by lkmklsmn • 930 • updated 17 months ago by croshong75 • 0
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Phasing genotype likelihood data and merging them with phased genotype calls data.
genotype likelihood phasing genotype calls written 17 months ago by Mr Locuace • 100
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Genotype phased and unphased
vcf phasing genotype snp written 17 months ago by manjumoorthy95 • 20 • updated 17 months ago by Pierre Lindenbaum ♦ 130k
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Genotyped SNPs were lost after michigan imputation server imputation and phasing
imputation michigan phasing written 21 months ago by Shicheng Guo • 8.3k
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