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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Soft-clipped reads and indel realignment #317

Open renzobalb opened 4 years ago

renzobalb commented 4 years ago

Hi everyone,

I was trying to post a question on the forum, but couldn't access it so I thought I'd post my questions here.

I was wondering whether:

a) You require soft-clipped reads to detect SVs using LUMPY (or whether hard-clipped reads are fine/ make no difference at all)? b) Whether you should perform indel realignment on the BAM files before running them through the LUMPY pipeline?

Thanks in advance