User: bha

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bha60
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Posts by bha

<prev • 43 results • page 1 of 5 • next >
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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 10 days 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 10 days ago by bha60 • updated 10 days ago by zx87545.3k
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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 4 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 4 months ago by bha60 • updated 3 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 5 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 5 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 5 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 5 months ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... Yes, i do have sample file as well. it's NOT zipped. here are the out files look like: http://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html#top ...
written 5 months ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... The genotype file is exactly in the same format you mentioned in above link, and haplotype is 0s and 1s in standard file. The genytpe look like: SNP1 rs1 1000 A C 1 0 0 1 0 0 SNP2 rs2 2000 G T 1 0 0 0 1 0 SNP3 rs3 3000 C T 1 0 0 0 1 0 SNP4 rs4 4000 C T 0 1 0 0 1 0 SNP5 rs5 5000 ...
written 5 months ago by bha60

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Popular Question 3 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 7 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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