User: bha

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bha10
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Posts by bha

<prev • 27 results • page 1 of 3 • next >
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simulation for genetic architecture using GBLUP
... I need to perform some simulation for genetic architecture (through GBLUP), the data set i am planning to use is 1000 G. Has anyone came across this? what should be the best software to do these simulation? ...
software next-gen population genetics written 1 day ago by bha10
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Comment: C: Remove snps with missing names
... yes, these are in VCF format. ...
written 12 days ago by bha10
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Comment: C: Remove snps with missing names
... How i can remove these IDs (".") from the the datasets? ...
written 12 days ago by bha10
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Remove snps with missing names
... I pruned the 1000G data with MAF, and some LD filtering. I wonder there are some snps with names as "." (snps indentifiers are as "." dot). Any suggestion how i should remove or pull out that ones? ...
genetics plink written 12 days ago by bha10
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Comment: C: Combine all chromosomes in a single file
... `bcftool concat` will be more appropriate? ...
written 15 days ago by bha10
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Combine all chromosomes in a single file
... I got 1000 genomes data which is in vcf format. All chromosomes (1 to 22) are in separate files. **Is there any way to combine all 22 chromosomes in a single file?** My final task is to prune that single file based on MAF and LD. I tried in PLINK (first convert everything in PLINK and tried to merg ...
genetics written 15 days ago by bha10 • updated 15 days ago by Bastien Hervé560
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Comment: C: Generating phenotype data
... Apologies for late reply. Actually i wanted to simulate the phenotype, but now i found some programmes which can do that, for instances, gcta, dissect etc. Many thanks for your message1 ...
written 7 weeks ago by bha10
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Generating phenotype data
... Same question is asked at stackoverflow, but other members asking to put it at this forum. sorry for repetition. I want to generate some phenotype data, example trait could be human height. The expression i want to use should be as: P corresponds to phenotype P ~ N (∑XiBi, δp) i couldn't di ...
R snp written 8 weeks ago by bha10
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Comment: C: How to convert plink.raw to map and ped files in any software
... I got two files 1) plink.raw (imputed genotypes as 012 format), and an other original map file say 2) plink.map file (which contain info for CHR, SNPIdentifier genetic distance and bpPOS). this is how i am doing; > famid <- FID patid <- IID fid <- PAT mid <- MAT s ...
written 5 months ago by bha10
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Comment: C: How to convert plink.raw to map and ped files in any software
... Yes, you are absolutely right. In original file, i have 3 heterozygous SNPs,but in current file (plink.raw 012) -this conflicting with original. I can't see 'G'. ...
written 5 months ago by bha10

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Popular Question 7 weeks 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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