User: Vincent Laufer

gravatar for Vincent Laufer
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Posts by Vincent Laufer

<prev • 158 results • page 1 of 16 • next >
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Comment: C: How to keep a log of columns removed from edited MSA?
... Please provide a sample of one of the input MSA files and the desired output file. ...
written 8 days ago by Vincent Laufer880
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Comment: C: Conditioning association summary statistics using a correlation matrix.
... @Jean-Karim - Thank you for your post. I will reflect on this. I will conduct a search on my own. However, if you have any manuscripts or even textbooks in mind, I will be sure to take a look at those too. ...
written 5 weeks ago by Vincent Laufer880
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Comment: C: Conditioning association summary statistics using a correlation matrix.
... Note, I posted a more technical (mathematical) description of the goal here: https://stats.stackexchange.com/questions/317310/using-correlation-structure-to-predict-association-strength-after-conditioning-o ...
written 6 weeks ago by Vincent Laufer880
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Conditioning association summary statistics using a correlation matrix.
... I am conducting a meta-analysis of genetic data, and I am also fine-mapping a few loci to try to determine which variants are the pathogenic or "causal" variants. In some of these loci, there have been studies done demonstrating at least one pathogenic variant, but in several of these cases there a ...
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Comment: C: Are WGS cohorts with large numbers of global participants (larger than 1kg) publ
... Huh. Nice. Was not aware of this resource. This is actually very close to what I need. If it had African populations broken down more, I would be good to go. Thank you very much for passing along. ...
written 7 weeks ago by Vincent Laufer880
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Are WGS cohorts with large numbers of global participants (larger than 1kg) publicly available?
... **The question:** Is there currently any way to get a larger number of whole genomes (in a subpopulation specific fashion) than is available through CGI or 1kG? If I could obtain, say 1000 YRI, 1000 CEU, and 1000 EUR genomes, I think I could get accurate enough estimates for my intended goals, but r ...
wgs 1kg 1000 genomes written 8 weeks ago by Vincent Laufer880
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Comment: C: What makes assigning A/T and G/C SNPs to a strand unreliable if MAF is not near
... I solved one of my questions. > Suppose we have a SNP rs1234 with A: 0.800 and T: 0.200, just how > unreliable is it to assign a strand using MAF? How likely it is depends on the size of the sample population. Suppose there are 1000 subjects in the sample and you wanted the know the probabil ...
written 5 months ago by Vincent Laufer880
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What makes assigning A/T and G/C SNPs to a strand unreliable if MAF is not near 0.5?
... Hello, I am attempting to do some fine-mapping experiments. To increase the chances of capturing the pathogenic variants, I would like to include as many variants as I can, including AT and GC SNPs, and 15% of my data seems like a lot to drop if it can be retained. I was reading from the Genotype ...
a/t g/c snp strand written 6 months ago by Vincent Laufer880
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Do imputed variants tend to show weaker, stronger, or the same average association compared to genotyped variants
... I was thinking about haplotype association analysis recently. I was thinking that a lot of haplotype association methods use an EM algorithm independent of case control status under the null of no association. I was then wondering if there are cases in which there are rare disease associated haplo ...
imputation genotyped snp gwas written 7 months ago by Vincent Laufer880
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Answer: A: SNP tools to infer copy number variations (CNVs)
... Alright, I'll try to break my answer into segments and hit everything. 1) Read Depth - You mention you've tried a lot of different techniques for Read Depth. Most good programs will include features for things like GC content, nucleotide variability, flanking regions, presence of repeats, etc. Howe ...
written 8 months ago by Vincent Laufer880

Latest awards to Vincent Laufer

Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: hypergeometric distribution for proximal gene enrichment
Scholar 8 months ago, created an answer that has been accepted. For A: Delete Text between two strings sed, awk
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling
Popular Question 9 months ago, created a question with more than 1,000 views. For Selection of a "suggestive" level of association in a GWAS study
Popular Question 11 months ago, created a question with more than 1,000 views. For List of causal variants for autoimmune diseases
Voter 11 months ago, voted more than 100 times.
Popular Question 12 months ago, created a question with more than 1,000 views. For Best implementation of negative binomial association test for GWAS data?
Popular Question 12 months ago, created a question with more than 1,000 views. For Rationale for including a certain number of PCs in a GWAS study?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling
Popular Question 15 months ago, created a question with more than 1,000 views. For Options for generation of publication quality gene diagrams with annotation
Popular Question 16 months ago, created a question with more than 1,000 views. For Options for generation of publication quality gene diagrams with annotation
Appreciated 17 months ago, created a post with more than 5 votes. For A: hypergeometric distribution for proximal gene enrichment
Student 18 months ago, asked a question with at least 3 up-votes. For List of causal variants for autoimmune diseases
Centurion 18 months ago, created 100 posts.
Popular Question 22 months ago, created a question with more than 1,000 views. For Options for generation of publication quality gene diagrams with annotation
Student 23 months ago, asked a question with at least 3 up-votes. For Rationale for including a certain number of PCs in a GWAS study?
Student 2.1 years ago, asked a question with at least 3 up-votes. For Rationale for including a certain number of PCs in a GWAS study?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: GWAS: low explained heritability
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: hypergeometric distribution for proximal gene enrichment
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: GWAS: low explained heritability

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