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VQSR and single sample processing
we have a database-centric exome-SNP-calling pipeline here that gains new samples over time. Hence we so far called SNPs on single samples.
As far as I understand your docs, this does conflict with VQSR since it seems to be designed for multi-sample vcf files.
Is there any recommended practice for single sample files? Will the approach work reliably at all, or do we have to combine lets say subsets of our samples to get good results?
Thanks for your help!