I'm quite new to genome sequencing and wanted to ask how to make a variant call file. I've been using Excel to organize my genome data and just wanted to know the process of getting the .vcf extension at the end of the file, so I can upload it onto genome analyses programs. Thank you!
If you're starting with WGS data, this is usually not done in R, but in previous steps of the workflow, for example with GATK HaplotypeCaller. There are a number of tools related to that task, doing it properly requires bioinformatics knowledge; you need to read about it quite a bit before running such a pipeline yourself. The keyword here is "variant calling".
If you have Excel files, that could mean that you already have the result of a pipeline (e.g. that someone else ran before), that could be for example obtained from filtering of the VCF. In that case the best is to ask the person who ran the pipeline to send you the VCF, which was an intermediary step.
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