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Post by Mete on Feb 2, 2014 5:14:04 GMT
Is it possible to use GCTA read in dosage file in MACH output format, filter is based on MAF and Rsquared and output in PLINK dosage format?
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Post by Jian Yang on Feb 20, 2014 8:17:38 GMT
Yes, for example,
gcta64 --dosage-mach test.mldose.gz test.mlinfo.gz --update-imput-rsq test.imput.rsq --imput-rsq 0.3 --maf 0.01 --make-bed --out test
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julio
New Member
Posts: 1 
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Post by julio on Mar 4, 2014 19:35:31 GMT
Is is possible to run a stepwise conditional analysis (massoc)on MACH dosage data? Is the massoc-file necessary for it?
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Post by Jian Yang on Mar 5, 2014 1:04:50 GMT
You may have to convert the MACH dosage data to PLINK files for doing the conditional analysis.
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Post by agri_bio on May 6, 2014 8:14:40 GMT
Yes, for example, gcta64 --dosage-mach test.mldose.gz test.mlinfo.gz --update-imput-rsq test.imput.rsq --imput-rsq 0.3 --maf 0.01 --make-bed --out test I tried to apply this command and it works fine, except of one output error in the bim file. My generated bim file does not contain the information about the chromosom (1st column) and position (4th column), only the second column (ID, in my case: chr_pos). e.g. 0 1_238 0 0 C T 0 1_300 0 0 A G instead of 1 1_238 238 0 C T 1 1_300 300 0 A G Do you have any advise how to solve this problem? |
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Post by Jian Yang on Jun 25, 2014 7:00:30 GMT
GCTA doesn't need chr and bp information to convert dosage data to best guess data. Are you using the latest version? I may need to see the log file.
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