Originally posted by sklages
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For Isaac2, here are the main changes:
- Split read support to facilitate SV detection (similar to BWA-MEM)
- Improved detection of ambiguous reference sequences (e.g. long repeats and pseudogenes)
- Improved indel recall and precision when using this version with the downstream caller (Starling)
- Support for BAM as input
- Various improvements in IO management and memory usage
- Bug fixes
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