User: Scott

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Scott80
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Posts by Scott

<prev • 32 results • page 2 of 4 • next >
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Answer: A: Retrieve Single Vcf From List Of Snp Rs#
... You can now also extract such data from the UCSC genome browser's Table Browser. http://genome.ucsc.edu/cgi-bin/hgTables Group: Variation Track: 1000G Ph3 Vars Specify a list of variants in rsID format under identifiers. ...
written 4.0 years ago by Scott80
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Comment: C: Problem with Haploview loading of files from latest (Sept 15-17 2014) update to
... Hi Mark, Yes. Sorry I never expanded on the last explanation. I couldn't get these files to work as they were. I had to manually edit the no calls. I ultimately ended up doing this with VCFtools instead. Were you having the same problem, or just interested? ...
written 5.0 years ago by Scott80 • updated 8 months ago by RamRS27k
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Comment: C: remove non biallelic SNPs from ped
... I just thought if they were originally in VCF format this would be easiest. I am most familiar with VCF, that's why I suggested this. I'm sure there are other ways.  ...
written 5.7 years ago by Scott80
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Answer: A: Linkage disequilibrium analysis of EUR populations from 1000 Genomes phase3 data
... After checking this manually it looks like all of the VCF files from Phase 3 of the 1000 Genomes Project obtained using the "data slicer" tool contain only non-related individuals.  ...
written 5.7 years ago by Scott80
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Comment: C: calculating LD for SNPs with more than two alleles
... Hi Adam. Thanks for the suggestion. I'm not sure if this is what I am looking for. Does this compute pairwise Chi-squared for each allele in any given SNP, with other SNPs? If so, I'm not sure how to integrate this data with R^2. A thorough explanation of what this option does would be great. Thank ...
written 5.7 years ago by Scott80
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Answer: A: calculating LD for SNPs with more than two alleles
... see comment ...
written 5.7 years ago by Scott80
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Answer: A: remove non biallelic SNPs from ped
... Not sure about your exact question, but in VCFtools you can quickly filter for only bi-allelic sites using: vcftools --vcf_file1.vcf --min-alleles 2 --max-alleles 2 --recode --out output_file_name.vcf ...
written 5.7 years ago by Scott80
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calculating LD for SNPs with more than two alleles
... How can multi-allelic (more than two alleles) SNPs be dealt with in LD analysis? I have used Haploview and VCFtools and I know these SNPs are excluded from the analysis. Ideally I would like to include these SNPs. Are there ways to treat each as multiple SNPs with different combinations of the allel ...
snps linkage disequilibrium ld multi-allelic written 5.7 years ago by Scott80 • updated 5.6 years ago by Biostar ♦♦ 20
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VCFtools LD calculations only for pairs that include a single SNP of interest
... I would like to calculate LD statistics for a VCF file using VCFtools. For the 1Mb window I am interested in, even using a R^2 minimum of 0.2, it is taking quite a bit of time to calculate these statistics. I am ultimately only interested in LD statistics that include a single SNP of interest. Is t ...
r^2 snp linkage disequilibrium vcftools ld written 5.7 years ago by Scott80 • updated 5.7 years ago by Adam1000
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Comment: C: How To Extract Random Snps From Whole Genome Data?
... the command `shuf` is not found when I try to run this on terminal in OSX. ...
written 5.7 years ago by Scott80 • updated 10 months ago by RamRS27k

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