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Diverging results between STAR and BWA aligned inputs #33

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Diverging results between STAR and BWA aligned inputs#33
@yasin-uzun

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@yasin-uzun
yasin-uzun
opened on Mar 7, 2023

Hi,

I am running squid with two types of inputs: 1) Samples aligned with STAR 2) Samples aligned with BWA

When using STAR output, I get less than 100 SV calls per sample. When I run with BWA output, I get several thousand SVs per sample. What is the source of this difference? Can you please give some information about this?

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