Hello all,
I am looking for a reliable, published tool for CNV discovery by differences in depth of coverage (DOC). Preferably something that accepts BAM as input. Our SV tool / pipeline (Hydra) works well for discovering breakpoints via paired-end mapping, but we (and others) find that certain classes of rearrangements are not easily detected by PEM yet are by DOC. In a previous study (Quinlan et al, 2010), we used an HMM on GC-corrected sliding windows, but would prefer to use a published method for a current study.
Could someone help me out with suggestions?
Best,
Aaron
I am looking for a reliable, published tool for CNV discovery by differences in depth of coverage (DOC). Preferably something that accepts BAM as input. Our SV tool / pipeline (Hydra) works well for discovering breakpoints via paired-end mapping, but we (and others) find that certain classes of rearrangements are not easily detected by PEM yet are by DOC. In a previous study (Quinlan et al, 2010), we used an HMM on GC-corrected sliding windows, but would prefer to use a published method for a current study.
Could someone help me out with suggestions?
Best,
Aaron
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