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sequencing pileup #98

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sequencing pileup #98

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Koeng101
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@Koeng101 Koeng101 commented Sep 5, 2024

this is code for doing real pileup sequence mutation calling. Attached are over 100 test sequencing pileups from a real run of mine, so this is what ACTUAL data will look like, with manual annotation of what I think is going on.

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Alrighty. So now I have a mutation caller than I think works. Now I just need to populate it with real data.

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Aight, so now I have a wtf moment. The pileup and sequence analysis from cs optional flags give me different results, but upon manual analysis, I trust the cs optional flags more. Maybe it's the quality scores that are impacting alignments?

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