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caitiecollins / treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
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Just a question: Can you recommend method for SNPs matrix generation? #57

Closed martinastoycheva closed 2 years ago

martinastoycheva commented 3 years ago

Hello,

I have ran treeWAS with a gene presence/absence matrix and it works fine so I wanted to try the SNPs as well but I am confused about the format that treeWAS requires and I was wondering if you can clarify a few things.

  1. Usually softwares generate vcf files when snp calling is performed so is there an easy way of converting a vcf file to the binary SNP matrix required by treeWAS?
  2. Do you recommend getting the SNPs from the alignment of the multiple genomes or by performing variant calling with something like Freebayes and then getting a consensus?
  3. Is there a pipeline or a recommended method that you tend to use in order to generate the SNPs matrix suitable for treeWAS?

Thank you for the help! Martina

hsinjou0714 commented 3 years ago

Hi Martina, I am also having this issue too. Have you found out a solution on converting vcf to matrix or a tool that may be good for treeWAS? Thank you, Christine

uyghbo commented 3 years ago

Hi Martina, I am also having this issue too. what did the ‘0’, '1', 'NA', mean in treeWAS data(snps)? Thanks