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Haplotype phasing and imputation in Beagle 5.1
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haplotype phasing related issues
written by kas •Dear members, How to code the alleles in a phased file to 0/1? `Selscan` is showing : ERROR: Alleles must be coded 0/1 only.
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Error in tmp_haplo[hap2_index, ] <- hap2
written by kas •Dear respected members, Anybody using "rehh" package, kindly help me. While calculating iHS values, its showing like this, hh_map <- data2haplohh(hap_file = "bta1__hapguess_switch.out", map_file = …
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Rehh package input files
written by kas •Dear respected members, How to make "map.inp" files for running rehh? I have .ped and .map files from plink. I have got the haplotype information …
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Imputation and haplotype phasing in Bovine 50K SNP data
written by kas •Hello everyone, I'm new to this haplotype phasing and imputation. I have plink output files (.ped, .map, .bed, .vcf). I don't know how to proceed …
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Haplotype Phasing with Shapeit2
written by SOHAILHi everyone, I am anew in haplotype phasing. I have 14 WGS individuals data from one human population and i want to perform Haplotype phasing …
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Do anyone have 64 bit version of fastPHASE
written by Being BioinformaticianRespected members, Do anyone have 64 bit version of fastPHASE. I have already written to author but what I get is 32 bit exe file. …
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Extended Haplotype Homozygosity Calculation
written by Being BioinformaticianRespected Members, I am new to Population genetics world and I am stuck while calculating extended Haplotype Homozygosity. Please help 1. Can I use output …
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how can I recode phased haplotype?
written by maryDear all I have reconstructed haplotype from fastPHASE for each chromosome, as you know it has 0 /1 code, is there any way to recode …
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Problems Installing Fastphase
written by mary<p>Dear all, </p> <p>I try to reconstruct haplotype by fastphase in my data, i download it from <a href='http://stephenslab.uchicago.edu/software.html'>http://stephenslab.uchicago.edu/software.html</a> for ubuntu 12.10. but I think …