* Updated some docker job scripts. * Added a script that converts some items in the VCF's INFO field into the sample field, to precipitate the need to merge multiple VCF files into a single multi-sample VCF, i.e., utilities/reformat_VCF2SEQC2.py. * No change to somaticseq algorithm.
2.4.0
* Restructured the utilities scripts. * Added the utilities/filter_SomaticSeq_VCF.py script that "demotes" PASS calls to LowQual calls based on a set of tunable hard filters. * BamSurgeon scripts invokes modified BamSurgeon script that splits a (proper) BAM file without the need to sort by read name. * No change to SomaticSeq algorithm
2.3.2
* Added run script generators for dockerized BAMSurgeon pipelines at utilities/dockered_pipelines/bamSurgeon * Added an error message to r_scripts/ada_model_builder_ntChange.R when TrueVariants_or_False don't have both 0's and 1's. * No change to SomaticSeq algorithm.
2.3.1
* Improved pipeline script generator, but still consider them experimental. * No change to SomaticSeq algorithm
2.3.0
* Changed some directory structures * Better integrated Strelka2
2.2.5
1) Will cat all the VCF files and use vcfsort.pl to sort if GATK.jar is not provided to do GATK CombineVariants. 2) Added a dockerfile.