Getting data into the proper format

[virpatel524]

Hi,

I was recommended to use your approach for determining COI with my malaria data. Unfortunately, I'm pretty new to VCF analysis, so I'm having some trouble understanding how to get my VCF files into your matrix format. First and foremost, how would you recommend converting my VCF files? Is there a script that does this easily? Second, what is the distinction between the major and minor allele and the reference and alternate allele? I know that they are not always the same when looking at VCF files, so I'm curious to know how you would go about accounting for this.

Thank you very much for your help!

[hhchang]

Thank you so much for your interest! I am not familiar with VCF files. I did some quick search and found that some existing codes can be used to change VCF file to tab delimited file (such as this one: https://github.com/EichlerLab/vcf-flow/blob/master/vcf_to_tab.py). You can give it a try and let me know if it works!

-Hsiao-Han