Hello!
Firstly let me say the support in this forum is amazing and we are very lucky to have you guys listen and respond to our issues!
I have illumina DNA sequening of bacterial populations which are paired, so 1 control condition and 1 experimental condition. I would like to create VCF's and then take away these "control" VCF variants from the "experiment" VCF's to leave me with novel variants in the experiments. Is there a method to do this?
I started off by joint genotyping however this gives only the variants shared by the two, so I think I need to created the VCF's separately and then filter the control VCF's from the experiment. Is that right? Does anyone have a method to do this in GATK or do I need to create the VCF's here and use another separate tool to do the filtering?
Thanks in advance!
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