Releases: icbi-lab/NeoFuse
v1.2.2a
v1.2.1
Multi-sample mode patch:
- Fixed a bug where a temporary file was improperly created in the working directory.
- Fixed a bug where an uninitialized variable would cause samtools sort to crash.
- Updated input TSV sanity checks.
- Multi-sample mode will now report the proper path to the output directory.
Thank you @kevinpryan for testing and reporting.
v1.2.0
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Updated Arriba to the latest version (v2.0.1).
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MHCflurry will now use pan models.
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NeoFuse can now accept VCF or tab-separated files with coordinates of structural variants found using whole-genome sequencing data, with the flag "-v". These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low confidence. (for more information please refer to Arriba manual).
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Flag "-S" can now be used with NeoFuse to determine how far a genomic breakpoint may be away from a transcriptomic breakpoint to still consider it as a related event. For events inside genes, the distance is added to the end of the gene; for intergenic events, the distance threshold is applied as-is. (Used with "-v" argument. Default: 100000).
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NeoFuse will now also report in the final output:
Split_Reads1 and Split_Reads2 : The number of supporting split fragments with an anchor in gene1 or gene2, respectively, is given in these columns. The gene to which the longer segment of the split read aligns is defined as the anchor.
Discordant_Reads : This column contains the number of pairs (fragments) of discordant mates (a.k.a. spanning reads or bridge reads) supporting the fusion.
Closest_Breakpoint1 and Closest_Breakpoint2 : When a matched whole-genome sequencing sample is available, one can feed structural variant calls obtained therefrom into Arriba (see parameter -d). Arriba then considers this information during fusion calling, which improves the overall accuracy. These two columns contain the coordinates of the genomic breakpoints which are closest to the transcriptomic breakpoints given in the columns breakpoint1 and breakpoint2.
(for more information refere to Arriba manual)
v1.1.3
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NeoFuse can now accept VCF or tab-separated files with coordinates of structural variants found using whole-genome sequencing data, with the flag "-v". These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low confidence. (for more information please refer to arriba documentation).
-
Flag "-S" can now be used with NeoFuse to determine how far a genomic breakpoint may be away from a transcriptomic breakpoint to still consider it as a related event. For events inside genes, the distance is added to the end of the gene; for intergenic events, the distance threshold is applied as-is. (Used with "-v" argument. Default: 100000).
1.1.2
- NeoFuse can now accept files containing known/recurrent fusions with the "-K" flag. Some cancer entities are often characterized by fusions between the same pair of genes. In order to boost sensitivity, a list of known fusions can be supplied using this parameter. Refer to Arriba documentation for more details.
- Arriba filters can be switched off with the "-f" flag. NeoFuse does not accept space-separated lists as arguments, use only comma-separated lists (in the form: "uninteresting_contigs,non_coding_neighbors,merge_adjacent", etc.). Refer to Arriba documentation for more details.
- Optimized BAM sorting for STAR output, "-l" flag will be removed in future versions.
v1.1.1
- NeoFuse can now handle large input files with the -l parameter.
- Fixed bug where '?' in the putative fusion protein sequence would return 0 cleaved peptides.
- Added feature for processing custom HLA lists (user-defined).
(see also https://icbi.i-med.ac.at/software/NeoFuse/NeoFuse.shtml)