User: vlaufer
vlaufer • 260
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Posts by vlaufer
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... 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 ...
written 4.5 years ago by
vlaufer • 260
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... 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 4.5 years ago by
vlaufer • 260
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... 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 ...
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Comment:
C: Batch load in haploview
... I suppose I should stipulate: Without using visual basic...
...
written 4.5 years ago by
vlaufer • 260
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... 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 ...
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... 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 ...
written 4.6 years ago by
vlaufer • 260
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... Ah - one caveat - suppose the ancestral information cannot be easily transformed into bed format?
...
written 4.6 years ago by
vlaufer • 260
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... 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 ...
written 4.6 years ago by
vlaufer • 260
• updated
4.6 years ago by
chrchang523 ♦ 4.6k
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... 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 4.6 years ago by
vlaufer • 260
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... 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 4.6 years ago by
vlaufer • 260
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For Background information and recommendations for phasing ASW whole genomes
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For A: VCF files: Change Chromosome Notation
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