User: Vivek
Vivek • 2.3k
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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 14 months ago by
Vivek • 2.3k
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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 14 months ago by
Vivek • 2.3k
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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 14 months ago by
Vivek • 2.3k
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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 14 months ago by
Vivek • 2.3k
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... If this is intended towards research, history of parental diagnosis would appear to be useful. ...
written 15 months ago by
Vivek • 2.3k
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535
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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 19 months ago by
Vivek • 2.3k
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535
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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 19 months ago by
Vivek • 2.3k
1
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1.0k
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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 23 months ago by
Vivek • 2.3k
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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 24 months ago by
Vivek • 2.3k
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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 2.5 years ago by
Vivek • 2.3k
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Scholar
9 weeks ago,
created an answer that has been accepted.
For A: Identify overlapping coordinates
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
Popular Question
10 months ago,
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For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
Teacher
12 months ago,
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For A: Identify overlapping coordinates
Teacher
14 months ago,
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For A: Identify overlapping coordinates
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16 months ago,
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For A: retrieving from ExAC in VCF format
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22 months ago,
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For C: data science courses, offered by John Hopkins University at Coursera
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2.1 years ago,
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For A: Identify overlapping coordinates
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For Identifying De Novo Variants In Trio Data
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For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
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For Identifying De Novo Variants In Trio Data
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For A: VCF files: Change Chromosome Notation
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For A: Identify overlapping coordinates
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2.5 years ago,
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For A: VCF files: Change Chromosome Notation
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For A: Phasing trios for identification of denovo variants
Scholar
2.5 years ago,
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For A: Identify overlapping coordinates
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For A: Identify overlapping coordinates
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2.7 years ago,
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For A: Identify overlapping coordinates
Teacher
2.7 years ago,
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For A: Identify overlapping coordinates
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For 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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For A: Phasing trios for identification of denovo variants
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3.0 years ago,
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For A: Identify overlapping coordinates
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