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No Split/Chimeric reads in Longranger/Lariat output #11

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mengshux opened this issue Feb 6, 2018 · 0 comments
Open

No Split/Chimeric reads in Longranger/Lariat output #11

mengshux opened this issue Feb 6, 2018 · 0 comments

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@mengshux
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mengshux commented Feb 6, 2018

I have noticed that in both the example WGS dataset NA12878 and our own WGS data, Longranger does not detect any split/chimeric reads. In my experience, this has caused problems in SV detection on getting the exact break points right. It seems that split read information is supposed to be incorporated into SV calls, since there are fields in both Loupe and the large_sv_calls.bedpe file to report them.
Since Longranger/Lariat uses BWA for alignment, and BWA-MEM and BWA-SW are both capable aligning split reads, my question is, are the current parameters that are being used taking advantage of this function?

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