ProTECT 2.5.0 is here with some great features (and a docker too)!
Major new features include:
- ProTECT can now start from checkpoints. Alignments are a thing of the past. ProTECT can now be run in the following ways -- a) fastqs trios, b) any combinations bam and fastq trios + haplotype (if at least one input is a bam), c) vcf + rna (bam or fastq) + haplotypes
- ProTECT now provides rudimentary support for peptides originating from fusion-gene events. Fusions will only be called from input RNA fastqs.
- ProTECT now implements an updated version of Transgene that optionally alllows the user to filter mutations for OxoG events.
- ProTECT now allows users to pull files directly from the NCBI GDC, using the file UUID and a valid download token.
- ProTECT allows users to only process a subset of "chromosomes" in the bam (This is useful if you want to drop the viral genomes in the GRCh338.d1.vd1 reference used by the GDC.
- ProTECT now has 2 additional reporting modules, describing the status of published immunotherapy-related gene networks in the sample, and the expression of CAR-T targets used in relevant clinical trials that are currently recruiting new patients.
- ProTECT now allows users to specify an email to receive completion updates per sample in a run.
Minor changes include:
- Fixed a small bug in processing MHCII peptide binding predictions using the sturniolo method.
- Bumped rankboost to 2.0.3 to handle edge cases where normal peptides weren't being handled correctly.
- Bams in the filestore are now deleted in a better fashion to reduce pressure on the file store.
- STAR is now sorted with samtools, fixing the --limitBAMsortRAM issue.
- Fixed a small issue with Transgene requesting teh wrong requirements.
- Updated resource requirements to increase efficiency.