Originally posted by honey
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For variant or given genomic regions, yes SVA will provide summary of read depth (and other quality measures for example SNP quality).
SVA can read SNV, indel, and large SV calls, together with their quality measures. However, I need to note that SVA itself is not a variant caller. It reads variant calls (generated by for example SAMTools), and annotate and visualize them.
All the best,
Dongliang
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