From Chasm Software Wiki
Known Issues with CHASM and SNV-Box
- Versions prior to 1.0.6: When mapping genomic coordinates, if multiple mappings could occur (due to alt splicing) snvGetGenomic randomly selected from possible mappings to missense mutations. This could result in different mappings from one run to the next for a small subset of mutations. This has been removed in version 1.0.6 to improve reproducibility.
- CHASM release 1.0.5 had a bug in snvGetGenomic that affected scoring of mutations submitted in genomic coordinates. Please upgrade to BugFix 1.0.5