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What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association with a report generation.

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    $\begingroup$ Have you tried omictools.com/gwas-category ? $\endgroup$
    – Failed Scientist
    Sep 4, 2017 at 11:13
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    $\begingroup$ thx, need 1 or two most relevant can`t experiment with a 100 of them $\endgroup$
    – player777
    Sep 4, 2017 at 17:15
  • $\begingroup$ Analysis of GWAS data generally requires quite a bit of data cleaning, as well as imputation, and the structuring of covariates. These are typically done on unix based clusters with some expertise in bioinformatics and are hardware resource intensive unless the number of subjects is very low. $\endgroup$
    – akaDrHouse
    Sep 5, 2017 at 17:31

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