User: vlaufer

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vlaufer250
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1 year, 11 months ago
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Posts by vlaufer

<prev • 33 results • page 1 of 4 • next >
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Burden tests in plinkseq (v0.08) running exponentially slower with more variants?
... Hello, I am implementing tests like the following in plinkseq (v0.08) pseq LOCUS assoc --tests calpha --perm 10000 --phenotype RA --mask loc.group=refseq maf=0.00:0.01 These run fine, and fairly quickly. However, if I change this latter test to: pseq LOCUS assoc --tests calpha --perm 10000 --phen ...
plinkseq statistics association genetics written 4.3 years ago by vlaufer250
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Comment: C: Making use of phased haplotypes in rare variant burden testing
... Brent - Thank you very much for sharing your code - very kind of you. I will accept this answer after a little time elapses, I do not want to discourage other answers. Note that you have the close parenthesis as part of the hyperlink, causing the link to fail without modification.   ...
written 4.3 years ago by vlaufer250
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Making use of phased haplotypes in rare variant burden testing
... Hello all, I have a GWAS cohort and a WGS cohort that is a subset of the GWAS cohort. I have identified all the lead SNPs from the GWAS data (larger n) and have defined linkage disequilibrium around each lead SNP in the study. Further, I have phased the WGS genomes. As such, I can determine the v ...
haplotypes gwas ngs burden phasing written 4.3 years ago by vlaufer250 • updated 4.3 years ago by brentp22k
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Comment: C: Batch load in haploview
... I suppose I should stipulate: Without using visual basic... ...
written 4.3 years ago by vlaufer250
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Batch load in haploview
... Here, at the Haploview website: http://www.broadinstitute.org/science/programs/medical-and-population-genetics/haploview/input-options  The docs instruct us that although ped files, etc cannot be viewed except in the GUI mode, there is a "batch file option" Does anyone know a work around to progra ...
commandline haploview written 4.3 years ago by vlaufer250 • updated 3.7 years ago by Biostar ♦♦ 20
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Tools that represent standard output from local ancestry estimation software visually
... The local ancestry tools with which I have worked typically output results like this: 11:51931933            01:339393929           00:1201542287 Meaning, for this chromosome, one copy is ancestry 1 from bp 1 to bp 51931933, at which point that chromsome goes from being ancestry 1 to ancestry 0. T ...
gwas ngs local ancestry visualize written 4.4 years ago by vlaufer250
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Comment: C: Filter according to a list of snps, setting SNPs not found in data as missing
... Ah - one caveat - suppose the ancestral information cannot be easily transformed into bed format? ...
written 4.4 years ago by vlaufer250
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Filter according to a list of snps, setting SNPs not found in data as missing
... I am calculating local ancestry using Lamp-LD. I have phased ancestral haplotypes of only those SNPs in 1kG that are also in Omni 1M produced. Some of these SNPs are not found in my GWAS data, which is currently in PLINK format, but the goal is to have an identical list of SNPs for both the ancest ...
missing plink snp gwas written 4.4 years ago by vlaufer250 • updated 4.4 years ago by chrchang5234.3k
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Comment: C: File Containing LD-Pruned SNPs with MAF in CEU and YRI populations?
... Hi Katie! Greetings from across the pond. Been working on this a lot today. I think I'll do the LD analysis using Haploview as you suggest, however there are lists of continent specific markers. The best compendium I have found so far is http://genetics.med.harvard.edu/reich/Reich_Lab/Datasets.html ...
written 4.4 years ago by vlaufer250
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Answer: A: Unique SNP sharing between populations
... Try this. Find the tool Lanc-CSV. It is a local ancestry estimation software.  Download their reference data files for each chromosome. Everything marked 1 2 or 3 is a continent specific marker. Everything marked -99 shows up in more than one population. take all of those files, do grep "-99" $ ...
written 4.4 years ago by vlaufer250

Latest awards to vlaufer

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Background information and recommendations for phasing ASW whole genomes
Good Answer 3.3 years ago, created an answer that was upvoted at least 5 times. For A: VCF files: Change Chromosome Notation
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Advantages of Biobase's TRANSFAC over and above what is freely available?
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: VCF files: Change Chromosome Notation
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Most effective way to merge individual VCF files into VCF files merged by chromosome
Supporter 4.3 years ago, voted at least 25 times.
Appreciated 4.3 years ago, created a post with more than 5 votes. For Making use of phased haplotypes in rare variant burden testing
Student 4.3 years ago, asked a question with at least 3 up-votes. For Making use of phased haplotypes in rare variant burden testing
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Linkage disequilibrium plots
Scholar 4.6 years ago, created an answer that has been accepted. For A: VCF files: Change Chromosome Notation
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Linkage disequilibrium plots

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