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CHANGELOG.txt
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CHANGELOG.txt
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# ctat-LR-fusion v1.0.0 Oct 8, 2024
- works well for both ONT and PacBio under default params.
- excludes alignment overlaps between gene pairs that fall within sequence-similar regions, and requires at least 25 bases (default) of exon overlap in the remaining regions.
- excluding neighbor-overlap gene pairings and additional annotation-based filtering between phase-1 and phase-2.
- added --FI_extra_params custom parameter to pass through STAR parameters to F
- included option for --examine_coding_effect
# ctat-LR-fusion v0.13.0 Jan 27, 2024
- allow for paralog alignments to be included
- pursue additional candidates where one breakpoint is initially <= MAX_EXON_DELTA and the other is within 1kb and there's multiple reads suggesting it.
- with multiple reads suggesting fusion, use the min value for the deltas in phase 1 for candidate selection.
- reorganization of preliminary candidate intermediate output formatting for easier tracking and troubleshooting of findings.
- igv-reports v1.11.0 which has default ordering of fusions according to descending read support in the html.
# ctat-LR-fusion v0.12.0 Jan 02, 2024
- igv html working with long and short reads together
- results sorted by descending countws of supporting reads
- in combined long/short mode, retain any fusion calls with illumina reads that meet the min read requirements regardless of dominant isoform fraction results
- added option --chim_candidates_only to just get the initial list of chimeric candidate
# ctat-LR-fusion v0.11.0 Oct 12, 2023
- leaner on disk space usage by sam->bam streamed
- include igv files bundle as output
- adding LeftGene and RightGene info thats retained on short read integration
- allow secondary alignments in phase 2 (important for retaining read support abundance across paralogs)
# ctat-LR-fusion v0.10.0 Aug 19, 2023
- more optimization of ctat-minimap2
- bugfix to ROI definition off-by-one on acceptor site for igv-report display
- include LeftGene and RightGene columns
- added get_MAS-seq_fusion_cell_barcoding.py for supporting sc-MAS-seq analysis (single cells and long reads)
# ctat-LR-fusion v0.9.0
- ctat-minimap2 update for chimeric reads
- includes default filtering at the 0.1 FFPM threshold
- igv-reports upgrade, better performance and highlight fusion breakpoints as ROIs
devel versions:
# --discarded-- (ctat-LR-fusion v0.8.0
- incorporates latest ctat-minimap2 with additional alignment filtering during chimeric mode for phase-1 of ctat-LR-fusion finding.
- (performance issues, do not use)
# ctat-LR-fusion v0.7.0
- included --min_FFPM (with default at 0.1), important when tackling massive data sets to avoid pursuing hundereds of thousands of candidates in phase 2.
# ctat-LR-fusion v0.6.0
- bugfixes for non-ref-splice coordinate assignments
- added option: --snap_dist <int> : if breakpoint is at most this distance from a reference exon boundary, position gets snapped to the splice site.
- added option: --min_frac_dom_iso_expr <float> : minimum expression of dominant isoform (default: 0.05)
- adjusted minimap2 alignment params used.
- exits gracefully if no fusions found in initial phase.
- cleaner organization of IGV-prep files.