Hello-
So, BWA samse randomly places reads which map to multiple locations equally well. Is there anyway to force BWA not to align such reads at all? I understand that randomly placing these reads makes sense in most cases since all locations score equally well; however, we are using NGS for medical diagnostics and our molecular geneticists will not sign out cases where reads are randomly placed. Their preference is for these reads to not be aligned at all, even if it means we have to Sanger sequence certain portions of genes. Any help would be appreciated, thanks!
So, BWA samse randomly places reads which map to multiple locations equally well. Is there anyway to force BWA not to align such reads at all? I understand that randomly placing these reads makes sense in most cases since all locations score equally well; however, we are using NGS for medical diagnostics and our molecular geneticists will not sign out cases where reads are randomly placed. Their preference is for these reads to not be aligned at all, even if it means we have to Sanger sequence certain portions of genes. Any help would be appreciated, thanks!
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