User: kas

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kas0
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Posts by kas

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Answer: A: Obtain VCF format file from imputed dosage format file using beagle2vcf
... have you got any solution? I'm also searching for this ...
written 15 months ago by kas0
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Which max-gap value will be suitable for Bovine 50K SNP chip data in selscan software?
... Dear members, I'm using Bovine 50K SNP data in which the distance bet 2 SNPs will be 50.6 kb. In selscan software, which value should I use for that **--max-gap** (i.e. maximum allowed gap between loci when assembling haplotypes for iHS; Default is 200, 000 bp)? ...
selscan selection signature ihs written 15 months ago by kas0
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Haplotype phasing and imputation in Beagle 5.1
... Dear members, Anybody elaborate on the steps for **haplotype phasing and imputation in Beagle v5.1**. I have plink format files (**.ped and .map**) and I tried the older version of Beagle (v3.3). It gives **.phased** as output. But I need **.hap** output files to use this as input for rehh package. ...
imputation beagle rehh haplotype phasing written 15 months ago by kas0
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Comment: A: haplotype phasing realted issues
... How to convert .phased to .hap file? ...
written 15 months ago by kas0
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Comment: C: haplotype phasing realted issues
... thank you for your response. I'm using beagle output (.phased files) as input for selscan ...
written 15 months ago by kas0
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haplotype phasing related issues
... 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. ...
selscan plink beagle written 15 months ago by kas0 • updated 15 months ago by ATpoint44k
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selection signatures using fst method
... Hello everyone, Does anybody has done the selection signature analysis using fst method (fixation index)? I have plink files (.ped and .map). Some softwares like hierfstat, genepop are there for doing this. But the manual is not in proper order. Please provide the steps to do those analysis starting ...
bovine snp data plink selection signatures fst written 16 months ago by kas0
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Error in tmp_haplo[hap2_index, ] <- hap2
... 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 = "12breedsmap.inp", allele_coding = "m ...
R fastphaseformat rehh ihs written 16 months ago by kas0 • updated 16 months ago by zx87549.9k
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How to label subpopulation in fastphase?
... Dear respected members, How to make subpopulation label file for haplotype phasing in fastPHASE? Please provide any example format. Thank you in advance ...
snp data fastphase haplotype phasing written 16 months ago by kas0
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Comment: C: Rehh package input files
... Thank you for your response. I've read the manual. Here totally 5 columns are there. Last 2 for ancestral and derived alleles. But I don't have that information. How to get those ancestral and derived alleles? If I load my map file in R, It's showing like this Error in read.table(map_file, r ...
written 16 months ago by kas0 • updated 16 months ago by zx87549.9k

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Popular Question 10 months ago, created a question with more than 1,000 views. For Haplotype phasing and imputation in Beagle 5.1

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