Use of VQSR when joint calling samples from targeted and whole genome sequencing
I'm interested in joint calling samples obtained through targeted sequencing and whole genome sequencing. Can anyone help me understand whether hard filtering or VQSR is most appropriate in this case? I understand that hard filtering is best for targeted sequencing and for whole exome sequencing with fewer than 30 samples, but what I want to do isn't so clear cut as either of those options.
Any insight would be helpful.
Thanks so much,
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