User: Veera

gravatar for Veera
Veera 90
Reputation:
90
Status:
Trusted
Location:
Denmark
Twitter:
doctorveera
Last seen:
1 year, 5 months ago
Joined:
3 years, 6 months ago
Email:
d****************@gmail.com


 

Posts by Veera

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Get number of variations in a huge VCF using Tabix?
... This is what I am looking for. Thanks :) ...
written 20 months ago by Veera 90
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How to analyse GWAS data for co-morbid disorders?
... Lets say I am running a GWAS for a disease condition O , where all my cases has one or more of the following diseases: A, B, and C, in addition to my outcome of interest O. So I include individuals with condition A, B and C in my control group as well. In the analysis I add covariates for A, B and C ...
pleiotropy gwas statistical genetics snp R written 21 months ago by Veera 90 • updated 20 months ago by Biostar ♦♦ 20
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How plink calculates the INFO scores ?
... The summary file from plink's `--dosage` command has a column 'INFO' with values about the imputation quality score. How does it calculates that? ...
dosage gwas plink written 2.1 years ago by Veera 90
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Simulate genotypes based on reference genotypes with same LD structure?
... If I have whole genome genotypes of, for example, 10,000 samples as reference data. Is it possible to simulate a gwas data (100 samples) with exactly the same LD structure as my reference gwas data ? ...
simulate plink ld genotype written 2.2 years ago by Veera 90 • updated 5 months ago by Shicheng Guo7.4k
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Answer: A: Understanding Conditional analysis
... Conditional analysis to identify the independently associated SNPs, can be done just with the summary statistics using GCTA software. (link: http://cnsgenomics.com/software/gcta/cojo.html) ...
written 2.2 years ago by Veera 90
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Answer: A: Finding SNPs in LD with GWAS hits
... You can use Broad Institute's SNAP tool to get SNPs in LD with your SNPs in specific populations. Just upload a list of SNPs, select the population and you'll get the output. https://www.broadinstitute.org/mpg/snap/ldsearch.php ...
written 2.8 years ago by Veera 90
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Answer: A: Use LD statistics to find proxy SNP
... You can find proxies for your snp using SNAP webtool from broad institute. Here's the [link][1] [1]: https://www.broadinstitute.org/mpg/snap/ ...
written 3.1 years ago by Veera 90
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Comment: C: Generating .ped and .map files from .dose.vcf.gz files
... Then you can read it through [plink2][1] [1]: https://www.cog-genomics.org/plink2/input#vcf ...
written 3.1 years ago by Veera 90
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Answer: A: Generating .ped and .map files from .dose.vcf.gz files
... I am not sure if your file is in dosage format or vcf format ! Assuming that you have a vcf file, you can straight away read with plink2 using `--vcf` argument and recode it ped and map files. If what you have is a dosage file, you convert it to plink format using [gtool][1] [1]: http://www.well.o ...
written 3.2 years ago by Veera 90 • updated 7 months ago by RamRS21k
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Subset dosage data
... How to subset a dosage file with a custom list of variants ? I need to extract the dosage information for a subset of variants from the main dosage file (imputed using IMPUTE2). Thanks   Update- I was able to do with GTOOL. ...
dosage impute2 plink gwas written 3.2 years ago by Veera 90

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Supporter 3.2 years ago, voted at least 25 times.

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