User: Vivek
Vivek • 2.2k
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PhD candidate, Genetics of complex traits.
Posts by Vivek
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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
Vivek • 2.2k
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... 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
Vivek • 2.2k
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... 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
Vivek • 2.2k
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... 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
Vivek • 2.2k
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... If this is intended towards research, history of parental diagnosis would appear to be useful. ...
written 4 months ago by
Vivek • 2.2k
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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
Vivek • 2.2k
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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
Vivek • 2.2k
1
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1
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493
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... 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
Vivek • 2.2k
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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
Vivek • 2.2k
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1.2k
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... 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
Vivek • 2.2k
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For A: Identify overlapping coordinates
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For A: retrieving from ExAC in VCF format
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