CTAT-VirusIntegrationFinder Release v1.5.0

• minor code updates for improved handling of read names that look like integers instead of strings.
• public release on Terra

Continues to be compatible with ctat genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

which uses STAR v2.7.8a as per: https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

** Download the FULL release, which contains all required submodules

ctat-VIF Release v1.4.0

CTAT-VIF Release v1.4.0

• turning off fraction unique flanking sequence filter by default
• include breakpoint and cigar alignment in duplicate read alignment definition
• under evidence read elimination: changing min read seq entropy to 0.75 from 1.5
• gzip chimJ outputs

Continues to be compatible with ctat genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

which uses STAR v2.7.8a as per: https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

** Download the FULL release, which contains all required submodules

ctat-VIF Release v1.3.0

• improved sensitivity and overall accuracy for virus integrations, allowing for multimapping reads.
• using STAR single-pass mode
• uses nr virus db, no repeat masking within virus db
• masking K113 in human genome in 2nd phase search.
• maxhits = 50
• virus integrations organized according to virus breakpoint coordinates.
• human genome insertions organized according to flanking sequence similarity
• low complexity insertion flank sequences filtered to further exclude likely false positives

Continues to be compatible with ctat genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

which uses STAR v2.7.8a as per: https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

** Download the FULL release, which contains all required submodules

ctat-VIF Release v1.1.0

v1.1.0 - Feb 22, 2022

• incorporated read cleaning step between STAR phases 1 & 2 involving trimmomatic and polyA-stripper. Can disable with --no_clean_reads parameter or using the wdl clean_reads boolean setting.
• splicing info added to report to indicate canonical splicing types
• breakpoint flanking sequences including candidate dinucleotide splice pairs are provided in output.
• final (refined) report restricted to those prelim entries that had non-zero recovered evidence reads.
• virus aligned bams are now restricted to proper pairs for PE reads.
• virus genome coverage content restricted to ungapped regions
• many revisions to Terra wdls to account for SE reads compatibility
• mitochondrial containing chimeric reads are auto filtered

** Download the FULL release, which contains all required submodules

CTAT-VIF RELEASE v1.0.1

Largely redesigned for further improved accuracy and general utility.

See updated installation instructions for latest setup info.

** download the FULL software package

ctat-VIF Release v0.1.0

Initial release for CTAT VirusIntegrationFinder (VIF)

Be sure to retrieve the 'FULL' version below.