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Add --calling_params '-q 15' to the tb-profiler profile command #257

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ryanjameskennedy opened this issue Jan 11, 2024 · 1 comment · Fixed by #268
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Add --calling_params '-q 15' to the tb-profiler profile command #257

ryanjameskennedy opened this issue Jan 11, 2024 · 1 comment · Fixed by #268
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@ryanjameskennedy
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With the current way of doing the qc in tbprofiler, we would likely weed out quite a few false minority variants if we add --calling_params '-q 15' to the tb-profiler profile command. This would remove a lot of the noise. This is slightly hacky since it would only work well on Illumina data generated with the new Q value binning system they started with on the NovaSeq.

@ryanjameskennedy ryanjameskennedy self-assigned this Jan 11, 2024
@ryanjameskennedy ryanjameskennedy added the medium Medium priority label Jan 11, 2024
@ryanjameskennedy ryanjameskennedy added this to the TB milestone Jan 11, 2024
@mhkc
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mhkc commented Jan 25, 2024

Seems from your description that that --calling_params '-q 15' might be too specific for a general rule. I think this is something that instead could go into the documentation and should be up to the individual users to configure.

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