User: Veera
Veera • 90
- Reputation:
- 90
- Status:
- Trusted
- Location:
- Denmark
- Twitter:
- doctorveera
- Last seen:
- 2 years, 2 months ago
- Joined:
- 4 years, 3 months ago
- Email:
- d****************@gmail.com
Posts by Veera
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... This is what I am looking for. Thanks :) ...
written 2.4 years ago by
Veera • 90
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... 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 ...
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... The summary file from plink's `--dosage` command has a column 'INFO' with values about the imputation quality score. How does it calculates that? ...
written 2.9 years ago by
Veera • 90
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... 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 ?
...
written 2.9 years ago by
Veera • 90
• updated
14 months ago by
Shicheng Guo • 8.0k
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... 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 2.9 years ago by
Veera • 90
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... 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 3.5 years ago by
Veera • 90
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... 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 3.9 years ago by
Veera • 90
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... Then you can read it through [plink2][1]
[1]: https://www.cog-genomics.org/plink2/input#vcf ...
written 3.9 years ago by
Veera • 90
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... 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 ...
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... 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.
...
written 3.9 years ago by
Veera • 90
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