User: soulsacross

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soulsacross60
Reputation:
60
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New User
Location:
Brazil
Last seen:
4 days, 20 hours ago
Joined:
6 years, 1 month ago
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s**********@gmail.com

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Posts by soulsacross

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Plot local ancestry on chromosome
... Hi, I have just posted an example karyoploteR code in [another post][1] [1]: https://www.biostars.org/p/167553/#384897 ...
written 5 weeks ago by soulsacross60
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Answer: A: Is there a tool to draw local ancestry plots per chromosome?
... Hi, although the topic is old, it might help people coming here to answer this very question. First use convertLAMPLDout.pl script that comes with LAMPLD to unwind haplotypes ` perl convertLAMPLDout.pl test_data/lampld.out test_data/lampld.out.long` Then use [this script][1] (see lait in http:// ...
written 5 weeks ago by soulsacross60
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Assessing phasing quality for unrelated individuals
... I am working with unrelated people for local ancestry inference and I was wondering what are the metrics to assess phasing quality when having no familial data. I got affy6.0 array data for some 90 individuals phased with shapeit using polymorphic sites panel available in https://mathgen.stats.ox.ac ...
genome snp written 9 weeks ago by soulsacross60 • updated 9 weeks ago by lieven.sterck5.5k
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Answer: A: searching tool for calculating switch/phase error rate
... Have you tried vcftools --diff functions? https://vcftools.github.io/man_0112a.html "COMPARISON OPTIONS These options are used to compare the original variant file to another variant file and output the results. All diff functions cannot be written to standard out. --diff-switch-error Used in co ...
written 9 weeks ago by soulsacross60
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Comment: C: searching tool for calculating switch/phase error rate
... Hi genomax, I took a look at the manual and it wasn't obvious to me which metric is homologous to switch error rate. ...
written 9 weeks ago by soulsacross60
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Answer: A: Obtaining LRR and BAF values from affymetrix SNP array
... Greetings from a Brazilian friend, I have successfully used this R package on a linux system to extract signal data from 6.0 arrays: https://bitbucket.org/brge/affy2sv/wiki/Home It says it can handle Axiom data as well. You could give a try. If using PennCNV downstream to that, the .log file on y ...
written 3.7 years ago by soulsacross60
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Comment: C: PennCNV and segfault error
... Hi, sorry I cannot help, but I would like to ask you if there's a link for this script pf yours, I am currently trying to use PennCNV for Axiom arrays. Thank in advance. :)  Kind regards ...
written 3.9 years ago by soulsacross60
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Answer: A: BIRDSUITE error ["could not open 'GenomeWideSNP_6.birdsuite_probelist' to read".
... Sorry for the amoumt of tex ...
written 5.1 years ago by soulsacross60
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BIRDSUITE error ["could not open 'GenomeWideSNP_6.birdsuite_probelist' to read".]
... Hi folks, I'm currently trying to use Birdsuite (http://www.broadinstitute.org/science/programs/medical-and-population-genetics/birdsuite/birdsuite-0) for CNV/SNP analysis and after installing it, I try to run like this: [code] /home/pedro/Desktop/BIRDSUITE/EXEDIR/birdsuite.sh --basename=AVC --ch ...
birdsuite snp cnv written 5.1 years ago by soulsacross60
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Comment: C: Snps In Linkage Disequilibrium For Ncbi Build 37 (Hg19)
... Hey! Thanks a lot for your answer! I was planning to do this as well later, since I was first geting a "test" set for running EIGENSTRAT. Well, I think I'll use for my sample the "--ld-window-kb" option in PLINK: http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml#ld2. Do you think this might suffic ...
written 6.2 years ago by soulsacross60

Latest awards to soulsacross

Popular Question 3.7 years ago, created a question with more than 1,000 views. For BIRDSUITE error ["could not open 'GenomeWideSNP_6.birdsuite_probelist' to read".]
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Snps In Linkage Disequilibrium For Ncbi Build 37 (Hg19)

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