Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data?
Hello, the Biostar community,
What I know about low coverage WGS (or shallow WGS) data is that it is an economic technique for genomic copy number detection in the realms of tumor diagnosis or prenatal diagnosis. However, is somatic single-nucleotide variation (SNV) could also be detected at such a low coverage? (5-10X)
I have a rough idea that a low coverage could greatly influence the F1 score.
However, is there, or could there be, a pipeline or methodology that could sacrifice sensitivity for acceptable specificity, or vise versa, to fit for special aims such as tumor diagnosis? I exhaustively searched for literature but ended up with nothing.
Could any scientist provide literature that I possibly missed or just convinced me that snv & indel calling in 5-10X WGS data is just theoretically infeasible?
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