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Removing overlapping variants from one VCF file from another?
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!