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fulcrumgenomics / fgsv

Tools to gather evidence for structural variation via breakpoint detection.
MIT License
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Progress logger can count templates with no primary alignment #9

Closed pamelarussell closed 2 years ago

pamelarussell commented 2 years ago

I'd question why we have a template with primary alignment, that seems like an issue with the input data.

This can happen if you filter a bam file on some criteria and lose the primary alignment of a template.