User: leeandroid

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leeandroid80
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Posts by leeandroid

<prev • 16 results • page 1 of 2 • next >
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Answer: A: PCA and statistics on SNPmatrix
... To pursue PCA you can use [SNPRelate][1] or [TASSEL][2] that has a user-frendly platform. [1]: http://corearray.sourceforge.net/tutorials/SNPRelate/ [2]: http://www.maizegenetics.net/tassel ...
written 12 days ago by leeandroid80
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Comment: C: DAPC different clustering results
... When running *find.clusters* the optimal number of clusters to retain is assessed based on BIC value and stored into *grp* same way as before. ...
written 6 weeks ago by leeandroid80
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Comment: C: DAPC different clustering results
... To run K = 2 to 20 you should use max.n.clust instead of n.clust, otherwise you are only runing k-means once. > n.clust an optinal integer indicating the number of clusters to be sought. If provided, the function will only run K-means once, for this number of clusters. If left as NULL, several ...
written 6 weeks ago by leeandroid80
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Comment: C: Retrieve list of kept SNP's after LD pruning
... Thank you for replying, Kevin. I was aware of the importance of chromosome nomenclature so I previously changed it to numeric values. Regarding variant ID's you're right. I was able to retrieve its original name by corresponding the row index in the snp_id_list to the row with the same index of the ...
written 9 weeks ago by leeandroid80
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Retrieve list of kept SNP's after LD pruning
... Hi everyone! I followed the [SNPRelate package tutorial][1] in order to filter a VCF by LD and finally pursued PCA. My problem is that by converting the VCF into GDS SNP's and Chromosomes ID's are also converted into a different nomenclature. >sample.id, a unique identifier for each sample. ...
vcf R gds snp snprelate written 10 weeks ago by leeandroid80 • updated 9 weeks ago by zx87544.5k
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Answer: A: From a vcf SNP file to a phylogenetic tree
... Try http://chibba.pgml.uga.edu/snphylo/ ...
written 3 months ago by leeandroid80
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Comment: C: Change sample names in vcf
... It works, cpad0112! Thank you for your precious help. ...
written 7 months ago by leeandroid80
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Comment: C: Change sample names in vcf
... Added header but not sure if in the right format. I'll try your solution and post if it worked. Thank you! ...
written 7 months ago by leeandroid80
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Comment: A: Change sample names in vcf
... Thank you all for replying! Seems that I failed to explain myself on the original post. The goal is to change the names of my samples like this: 123_4:A7TT6AKXX:1:1000000001 > 123 ABC100:A7TT6AKXX:1:1000000001 > ABC100 Eventually I was able to change them using bcftools reheader* - like Pie ...
written 8 months ago by leeandroid80
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Change sample names in vcf
... Hi everyone. I want to simplify the names of the samples of a VCF file by removing the suffix that was added during sequenciation but i am not being successful. Right now my samples are named like this: 123_4:A7TT6AKXX:1:1000000001 or ABC100:A7TT6AKXX:1:1000000001 In the first case I want to ...
vcf sample name written 8 months ago by leeandroid80

Latest awards to leeandroid

Scholar 12 days ago, created an answer that has been accepted. For A: PCA and statistics on SNPmatrix
Popular Question 3 months ago, created a question with more than 1,000 views. For Change sample names in vcf

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