The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Its mentioned in the VQSR documentation that in order to achieve the best results, we need to call variants with at least 30 samples each time and then apply VQSR on the whole dataset. In our lab we only multiplex 4 exome samples in a run. Does this mean that for every single run I need to add 26 additional exome samples and call variants and then apply VQSR to the entire data set? Is it not recommended to run VQSR on single exome VCF file? Are there any other options for me ? (except hard filtering of variants)