User: bha

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bha60
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Posts by bha

<prev • 45 results • page 1 of 5 • next >
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Comment: C: Phenotype from plink fam file in gcta
... Many thanks Kevin, but basic point was that if phenotype is already in test.fam, then what is point to have separate --pheno test.phen. Anyways thanks for responding ...
written 10 months ago by bha60
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Phenotype from plink fam file in gcta
... My question is about specifying phenotype file in GCTA analysis. My phenotype data is in my .fam file(sixth column). But software notes says i should make another test.phen. is it possible that GCTA read phenotype from .fam file? # MLMA analysis - If you have already computed the GRM gcta6 ...
snp gcta written 10 months ago by bha60 • updated 10 months ago by Kevin Blighe48k
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Comment: C: How to convert bgen data files to PLINK format
... I tried this: plink2 --bgen data.chr22.bgen --make-bed --out ex22 But got this error message: Error: .bgen file does not contain sample IDs, and no .sample file was specified. what am i missing in command? ...
written 11 months ago by bha60
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How to convert bgen data files to PLINK format
... I have sequence data which is in [.bgen format][1] . Wanted to convert this into PLINK format. Any suggestion what's the best way to do this? [1]: http://www.well.ox.ac.uk/~gav/bgen_format/ ...
software bgen plink written 11 months ago by bha60 • updated 10 months ago by Biostar ♦♦ 20
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How to Ranking SNPs
... I have SNPs data sets in PLINK format. I wanted to choose top 1000 only (based on p-value or some other order). I wonder, can i do this in PLINK? Or any other programme can do this SNP ranking? Any suggestion please? ...
R plink snp written 15 months ago by bha60
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check relatedness of individuals
... I used 1000 g data sets to simulate the sequence. After performing simulation, I got 10K individuals, for some other analyses. I wonder, how i can check the relatedness of simulated individuals with original data (individuals)? Should I first calculate simple correlation of MAF from two data sets or ...
R next-gen genetics plink snp written 16 months ago by bha60 • updated 15 months ago by Biostar ♦♦ 20
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Comment: C: How to convert Haplotypes file to PLINK format data
... yes, i think it works well. ...
written 16 months ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... Seems like that GTOOL can do this conversion: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#formats ...
written 16 months ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... Yes, essentially they are. I have both genotypes, and haplotypes files. My main concern is to convert them to PLINK format, either haplotype or genotypes. Any idea please? ...
written 16 months ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... these probabilities are 0s and 1s. And haplotypes are also in 0s and 1s. what do you suggest? ...
written 16 months ago by bha60

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Popular Question 14 months ago, created a question with more than 1,000 views. For How to convert plink.raw to map and ped files in any software
Popular Question 19 months ago, created a question with more than 1,000 views. For How do I remove duplicated by position SNPs using PLink?

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