User: Vivek

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Vivek2.2k
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PhD candidate, Genetics of complex traits.

Posts by Vivek

<prev • 234 results • page 1 of 24 • next >
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Comment: C: Position error using write.plink
... Can you also post the map file you are using here? `snp.data = smc_test$map` Is there a discordance between your snp.data and this map? ...
written 3 months ago by Vivek2.2k
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Comment: C: GWAS data analysis strategy or pipeline
... I'm not sure what you mean by p_hat, the admixture QC is done with some PCA analysis and a reference population like 1000 genomes. There must be a tutorial on biostars if you search for it. You remove any samples related more than third degree using KING for kinship analysis. ...
written 3 months ago by Vivek2.2k
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Comment: C: GWAS data analysis strategy or pipeline
... When you use a linear model to check for association (Y = XB + E) the core assumption is that the elements of Y are independent, that's why you check for kinship and admixture and remove any that violate those assumptions. ...
written 3 months ago by Vivek2.2k
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Answer: A: GWAS data analysis strategy or pipeline
... The phase and impute strategy would work if you have a genome wide array of markers. There won't be enough genome wide SNP coverage to impute accurately if all you have is an exome array. The other option is to go with weighted burden tests, finding something from them is a question of how much powe ...
written 3 months ago by Vivek2.2k
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Comment: C: Longitudinal Health Record Database Structure
... If this is intended towards research, history of parental diagnosis would appear to be useful. ...
written 4 months ago by Vivek2.2k
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Comment: C: vcf file processing
... There are more elegant solutions if you can do some scripting but here's a crude workflow: If you have one line per gene in the bed file, you can initially split the BED file into one file per gene like this: split -l 1 Genes.bed Genes- Depending on the number of genes, you might produce a l ...
written 8 months ago by Vivek2.2k
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Comment: C: vcf file processing
... Are you trying to extract them into separate files per gene or are you trying to run a burden test or something sophisticated? ...
written 8 months ago by Vivek2.2k
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Answer: A: How to generate text file having SNP list from bim file in plink?
... awk '{print $2}' your_file.bim > snplist.txt Would work to give you a SNP list but I don't clearly understand what you are trying to do after that. If you are looking to subset a dataset for individuals you need to specify the individuals you want to keep/remove to PLINK. ...
written 11 months ago by Vivek2.2k
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Answer: A: Individual chromosome SNP VCF
... You could download a subset with tabix for the regions you need. tabix -h ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz '2:39967768-39967768' > dbsnp_2_39967768_39967768.vcf ...
written 12 months ago by Vivek2.2k
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Answer: A: Calculating ethnicity of a sample VCF
... To find the ethnic sub group your sample falls in, you could pick a set of common SNPs (MAF > 5% within each sub-population group) common to your sample and the 1000 genomes data. Do a PCA of the 1000 genomes samples using eigenstrat's smartPCA and project your sample into that pre-computed space ...
written 18 months ago by Vivek2.2k

Latest awards to Vivek

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: retrieving from ExAC in VCF format
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: data science courses, offered by John Hopkins University at Coursera
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Good Question 15 months ago, asked a question that was upvoted at least 5 times. For Identifying De Novo Variants In Trio Data
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: data science courses, offered by John Hopkins University at Coursera
Popular Question 16 months ago, created a question with more than 1,000 views. For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
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Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
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