![]() ![]() ** Download the FULL tar.gz file, which contains all required submodules ** human-specific refinements: IGH and IGL super-loci now include intergenic regions included upstream regions as targets for CRLF2, DUX4, and MALT1 known to fuse w/ IGH in cancer hard-masking DUX4-paralogs and pseudogenes that confound IGH-DUX4 fusion calling (ideas inspired by FusionCatcher so certain important known cancer-relevant fusions aren't missed, even when the data likely stem from contaminating DNA rather than true RNA-based reads).Ĭompatible CTAT genome libs are available here: The BRAF/AKAP9 fusion was falsely excluded by the previous STAR-F release, and now properly recaptured again in this release). This was found to be particularly relevant to excluding blast-homology detection between BRAF and AKAP9 in gencode v31 where additional transcript annotations in both genes extend into Alu elements and would otherwise be detected as false homology. Because of repbase licensing requirements, its more straightforward to just use Dfam with nhmmer for identifying human-homologous repeat elements and softmask them prior to blast. (this is similar to the earlier repeatmasker approach used in earlier versions of STAR-Fusion. use Dfam-based masking of cds-plus database prior to blast & homology detection. allow exceptions to requirement of breakpoint-defining reads such as IGH-CRLF2 where breakpoints may be ill defined given complex structural rearrangements. ![]() bugfix for RT-artifact removal, no longer case sensitive on splice dinucleotides
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