CTAT-Mutations Release v4.3.0

4.3.0 June 29, 2024

• bugfix w/ cigar-N-splitter, incorporating the required read group ID in each alignment entry - impacts long read calling sensitivity

• for faster workflow, set default boosting to 'none' and turned off blat_ED and annot pass annotations unless boosting is indicated.

• ctat mutation wdl and Terra wrapper wdls updated

• added bamsifter and strand-specific read normalization

• replace gatk cigar-N-splitter with our own pysam based version

• add ctat-mutations to dockstore for easy integration into terra or other supported cloud platforms

CTAT-Mutations v4.1.0 Release

4.1.0 March 13, 2024

• incorporated support for single cell transcriptomics
• more robust accounting of read support per variant type including indels and multithreading
• include HC-realigned bam file as an output.

uses CTAT genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

Use our singularity or docker images for easy execution: https://github.com/NCIP/ctat-mutations/wiki/ctat_mutations_docker_singularity

CTAT-Mutations Release v4.0.0

• included preliminary support for pacbio rna-seq (operational, but not benchmarked): use --left <pbio.fastq> and --is_long_reads
• turned off boosting by default
• when boosting on, adds boosting annotations instead of filtering (vcf annotation of BOOSTselect)
• boosting of indels turned off, only boosting on snvs
• added ctat-genome-lib-builder submodule, incorporated minimap2 index prep
• cravat data resources provided as tarball and documentation for installation updated.

uses CTAT genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

Use our singularity or docker images for easy execution: https://github.com/NCIP/ctat-mutations/wiki/ctat_mutations_docker_singularity

CTAT-Mutations-v3.3.1

v3.3.1 Jan 22, 2023

• greatly improved memory usage around the annotate BLAT ED step

uses CTAT genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

Use our singularity or docker images for easy execution: https://github.com/NCIP/ctat-mutations/wiki/ctat_mutations_docker_singularity

CTAT Mutations v3.3.0

3.3.0 Dec 8, 2022

• support for providing target interval list (eg. just search exome regions)
• local wdl imports so not requiring network connection on secure systems.
• further improvements for parallelization and memory usage (annotate_PASS_reads.py)

uses CTAT genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

Use our singularity or docker images for easy execution: https://github.com/NCIP/ctat-mutations/wiki/ctat_mutations_docker_singularity

CTAT-Mutations v3.2.0

3.2.0

• revised WDLs for simpler configuration with Terra
• using all common variants for training ML in boosting
• drop SPLICEADJ, now just using DJ
• now explicitly writing feature matrices for use with the downstream ML steps for improved transparency and flexibility
• our RVBLR and py-snpir are now available as submodules, although not fully integrated into the ctat_mutations, and also leverage feature matrices as above.
• uses CTAT genome lib: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/

v3.0.0

• improved boosting performance
• rewrote workflow logic using WDL
• run 'make' in the base directory to install Cromwell workflow runner
• moved RVBLR (RVBoost) to https://github.com/broadinstitute/RVBLR

This version is compatible with CTAT genome libraries here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.9/

CTAT-mutations Release v2.5.0

2.5.0
-leverages Open-CRAVAT for annotations in place of REST-call to web app.
-incorporates additional boosting methods: SGBoost, GBoost, AdaBoost, and RF
-cleaner organization of output files
-added gnomad pop AF annotations
-added clinvar annotations
-igv-reports incorporates clinvar and FATHMM
-cancer-related variants selected based on chasm & vest pvals, or FATHMM or clinvar pathogenic attributes.

CTAT-mutations Pipeline v2.4.0

2.4.0
-added support for using single-end rna-seq reads
-support for RVBLR (our RVBoost-integration as RVB-like R)
-pctextpos is computed as an annotation and leveraged by RVBLR
-more robust variant annotation / multithreading
-annot_PASS_reads on by default now (again), but there's an option to disable if necessary.
-various bugfixes

CTAT-Mutations Release v2.3.0b

CTAT-mutations was heavily revised to focus on first annotating all variant sites followed by extraction of likely cancer-relevant mutations.

Singularity image is provided at: https://data.broadinstitute.org/Trinity/CTAT_SINGULARITY/

See wiki documentation for usage info.