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Failure to call well-known fusions on WES samples #311

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maximus3219 opened this issue May 24, 2023 · 0 comments
Open

Failure to call well-known fusions on WES samples #311

maximus3219 opened this issue May 24, 2023 · 0 comments

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@maximus3219
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I have performed WES on multiple dermatofibrosarcoma protuberans (DFSP) samples with known COL1A1::PDGFB fusion.
However manta fails to call this translocation on all the samples.
I have changed the two values 'minEdgeObservations' and 'minCandidateSpanningCount' in the manta configuration file to 2.
And supply --callRegions with the targeted regions.

Is there any way to further increase the sensitivity?
Also, is there anyway I can annotate the translocation with the gene names? Occasional samples have call of translocation involving t(17;22), but the genomic location seems to be falling out of COL1A1 and PDGFB gene, respectively. Not sure if they are the correct calls.....

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