User: kl

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kl0
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Posts by kl

<prev • 25 results • page 1 of 3 • next >
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Match:0 michigan imputation server output
... Hello, I've ran an imputation job successfully. However, I thought match:0 is strange. What does it mean exactly? Skip allele frequency check. Calculating QC Statistics Statistics: Alternative allele frequency > 0.5 sites: 296,279 Reference Overlap: 100.00 % Mat ...
michigan imputation server written 10 days ago by kl0 • updated 10 days ago by Bastien Hervé4.7k
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Comment: C: How can you update vcf when one of the columns is CHR:POS:REF:ALT using bcftools
... It does - the ID column is CHR:POS:REF:ALT. ...
written 10 days ago by kl0
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How can you update vcf when one of the columns is CHR:POS:REF:ALT using bcftools?
... Hello, How can you replace the column that is CHR:POS:REF:ALT as rsid name using BCFtools for a vcf v4.2 file? Many thanks ...
bcftools written 12 days ago by kl0
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Comment: C: michigan imputation server
... Hi, I have imputed my data using minimac4 on the Michigan imputation server. Is Dosage convertor the only way to produce plink files? I have tried doing this using plink --vcf but it provides an odd output like this (where 2nd column has chr:pos:A1:A2;snp) - basically an invalid bim file. 22 ...
written 23 days ago by kl0 • updated 23 days ago by genomax87k
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Comment: C: Post-imputation steps (cleaning and converting to plink)
... Yes, I'm not tech-savvy so it makes it even more tiring! So, I've closed it into my directory using Git and then, the next step is downloading cget. I do this in the directory of DosageConvertor (not sure if this is what is needed but it is unclear) pip install cget Requirement already ...
written 23 days ago by kl0 • updated 23 days ago by Kevin Blighe63k
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Comment: A: Post-imputation steps (cleaning and converting to plink)
... I think I've tried that before but couldn't get it work as it needs a C++ library which I couldn't seem to install. I'll try and see if I can figure it out if its the only way to convert! Thanks for the advice. ...
written 23 days ago by kl0
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Comment: C: Post-imputation steps (cleaning and converting to plink)
... Hmmm.. I've found some commands to annotate and convert to plink. However, the output is definitely not a correct plink .bim file! I tried to also just convert into plink without annotating (in case that caused it) but the same thing happens. the second column is chr:pos:A1:A2:snp or chr:pos:A1:A2 ( ...
written 23 days ago by kl0 • updated 23 days ago by RamRS28k
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Comment: A: Post-imputation steps (cleaning and converting to plink)
... The files downloaded from the Michigan server are v4.1 using minimac4. ...
written 23 days ago by kl0
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Comment: A: Post-imputation steps (cleaning and converting to plink)
... Hmmm.. I've found some commands to annotate and convert to plink. However, the output is definitely not a correct plink .bim file! I tried to also just convert into plink without annotating (in case that caused it) but the same thing happens. the second column is chr:pos:A1:A2:snp or chr:pos:A1:A2 ...
written 23 days ago by kl0 • updated 23 days ago by genomax87k
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Post-imputation steps (cleaning and converting to plink)
... Hi, I have just finished imputing my genetic data on the Michigan server (filtered on r2=0.3) and I want to convert to plink. What are the next steps such as cleaning and converting to plink? Anyone have any useful scripts and to do this over all chromosomes? Any advice would be much appreciated! ...
snp michigan imputation server written 28 days ago by kl0

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