Dear Biostars, please help us to understand something. When and why to create a VCF file? Is it mandatory to create a VCF file for every single project or only when someone uses a different reference genome? Me and my colleague are making SNP analysis from Mutation Accumulation Lines (MAL) experiment. We are following a workflow and in the early MAL experiments, people used a VCF file that has been created for reference genome version 3.0 but we are using reference genome 4.0 and therefore we are creating a new VCF file. What we are wondering is that, can we also use that VCF file that has been created for reference genome 4.0 for another MAL experimental data by using the same reference genome? Is that file strongly dependent on reference genome or the data that we are using?
This is if you have exactly the same sample input for the vcf files and the same reference genome, if different, make new vcf files:
a VCF file is a variant calling format, it contains all of the variants called between a sample and a reference. If you are using the same reference they used to call their variants, then yes you can use the same VCF but if you are using a newer reference then no do not use the same VCF file of the older version, there may be differences between the two reference genomes and therefore the VCF file.
Thank you very much. I was hoping to hear that. You made my day!