User: Vincent Laufer

gravatar for Vincent Laufer
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Posts by Vincent Laufer

<prev • 152 results • page 1 of 16 • next >
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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 12 weeks ago by Vincent Laufer870
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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 3 months ago by Vincent Laufer870
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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 4 months ago by Vincent Laufer870
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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 5 months ago by Vincent Laufer870
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Comment: C: QTL mapping vs. Association mapping for bi-parental crosses
... Hi Matthias, I suspect this old post will give you a lot of the info. you need. If it does not, I will try to provide any further answers you require: https://www.biostars.org/p/47725/ ...
written 5 months ago by Vincent Laufer870
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Comment: C: SNP tools to infer copy number variations (CNVs)
... Hey Ceru, I will provide an answer, but I need more information first. 1) Is this NGS sequencing data, or DNA microarray (chip) data. If so, what kind (e.g., whole genome sequencing, exome only, or what; and what company; or if chip data, what's the chip). 2) Do you have other genetic data on thes ...
written 5 months ago by Vincent Laufer870
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Comment: C: popoolation parallelization problem
... hmm. if the problem isnt with file handling in their scripts, my next most likely guesses are: 1) system resource requests on your cluster 2) file handling in your scripts 3) system resource allocation on your cluster ...
written 5 months ago by Vincent Laufer870
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Comment: C: popoolation parallelization problem
... have you tried looking at temporary files that popoolation generates, or better yet at the code to see how it generates them? ...
written 5 months ago by Vincent Laufer870
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Comment: C: Report haplotype frequencies from a region within a phased vcf file
... Not that I see from a quick search of the net, but you are right to post it on a blog like this cause people have almost certainly done it. I would: 1) download 1kg phased VCF file 2) trim to just the SNPs I wanted 3) convert into my desired input format for Haploview (https://www.broadinstitute.o ...
written 5 months ago by Vincent Laufer870
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Comment: C: Identify recessive conditions from VCF files
... It *IS* possible to determine phase for some variants using a VCF file. Many phasing algorithms, for example the BEAGLE suite, will actually take a VCF as the input file without modification. https://faculty.washington.edu/browning/beagle/beagle.html https://faculty.washington.edu/browning/beagl ...
written 5 months ago by Vincent Laufer870

Latest awards to Vincent Laufer

Scholar 5 months ago, created an answer that has been accepted. For A: Delete Text between two strings sed, awk
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling
Popular Question 6 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 8 months ago, created a question with more than 1,000 views. For List of causal variants for autoimmune diseases
Voter 8 months ago, voted more than 100 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For Best implementation of negative binomial association test for GWAS data?
Popular Question 9 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 9 months ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling
Popular Question 12 months ago, created a question with more than 1,000 views. For Options for generation of publication quality gene diagrams with annotation
Popular Question 13 months ago, created a question with more than 1,000 views. For Options for generation of publication quality gene diagrams with annotation
Appreciated 14 months ago, created a post with more than 5 votes. For A: hypergeometric distribution for proximal gene enrichment
Student 15 months ago, asked a question with at least 3 up-votes. For List of causal variants for autoimmune diseases
Centurion 16 months ago, created 100 posts.
Popular Question 20 months ago, created a question with more than 1,000 views. For Options for generation of publication quality gene diagrams with annotation
Student 20 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 22 months ago, asked a question with at least 3 up-votes. For Rationale for including a certain number of PCs in a GWAS study?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: GWAS: low explained heritability
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: hypergeometric distribution for proximal gene enrichment
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: GWAS: low explained heritability
Scholar 2.2 years ago, created an answer that has been accepted. For A: GWAS: low explained heritability
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: hypergeometric distribution for proximal gene enrichment

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