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EichlerLab / smrtsv2

Structural variant caller
MIT License
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Is the `Align` step required? #41

Closed SHuang-Broad closed 4 years ago

SHuang-Broad commented 4 years ago

Hi,

I am tasked running the SMRT-SV-2 algorithm and compare its performance against several long read SV callers. Reading the read me and the publication on SMRT-SV, I am wondering if this alignment step is a required step, or can it be skipped if the PacBio (HiFi) read has already be aligned (minimap2) to the desired reference?

Thanks! Steve

paudano commented 4 years ago

If you have the alignments, create a file with paths to the BAM(s): align/alignments.fofn

The pipeline should pick it up from there. Let me know if you have any trouble with it.