v2.3

Version 2.3 includes:

1. handling of CRAM and BAM files.
2. A nextflow script to assist the building of Panel-of-normals (mutect_build_pon.nf).
3. Update to GATK 4.2.
4. Docker containers were updated (iarcbioinfo/mutect-nf:v2.3, iarcbioinfo/mutect-nf:v2.3_gatk2, and iarcbioinfo/mutect-nf:v2.3_gatk3)
5. Singularity containers are built directly from docker containers.

v2.2b

Minor release. Improves SM field convention to avoid clashes when doing multi-sample calling with RNA-seq

v2.2

Added new functionality:

• added option --filter_readorientation that uses gatk's LearnReadOrientationModel in filtering step (for gatk4)

Minor changes:

• corrected source for docker container (previously on nalcala instead of IARCbioinfo)
• debug multi-sample
• ensures that symlinks to split beds are created (helps running with singularity)
• correctly set up deploy of dags produced during circleci tests to github
• change tempdir for sort for smoother use of singularity
• improved readme with schematic workflow

v2.1

Added new functionalities:

• gatk4 support; gatk versions <=4 are still supported as in v1.0 but the pipeline is now not actively developed for them
• conda environments, Dockerfiles, and Singularity files for gatk2, gatk3, and gatk4 and their profiles in nextflow.config
• genotype mode (gatk4 only) on positions from a VCF (see help)
• RNA-seq preprocessing for genotyping option (using gatk SplitNCigarReads and custom python script)
• tn_file input mode now can include extra parameters specific to the genotype option (vcf for genotyping, and preprocessing of RNA-seq; see help)
• allows multisample calling and genotyping; this requires tn_file input mode, and is automatically done when multiple rows in the tn_file have matching sample names
• contamination estimation and filtering option (gatk4 only)
• panel of normals option (gatk4 only)
• now uses circleci 2

Minor changes:

• parameter out_folder is now output_folder
• parameter dbsnp is now known_snp
• parameter bam_folder has been removed! now tn_file must specify the exact location, not the location relative to bam_folder
• parameter gatk_version must be specified to use old version of gatk (default is 4)
• prints params in log

v1.0

First release of pipeline. Supports Mutect1 and 2 up to gatk3.