* No guarantee if cram files are compatible with the individual mutation callers. * Also fixed a bug where variants called by Strelka only were not considered, though this would not change the results much as Strelka-only somatic calls are very rare.
2.7.1
* Without --gatk $PATH/TO/GenomeAnalysisTK.jar in the SomaticSeq.Wrapper.sh script, it will use utilities/getUniqueVcfPositions.py and utilities/vcfsorter.pl to (in lieu of GATK3 CombineVariants) to combine all the VCF files. * Fixed bugs in the docker/singularities scripts where extra arguments for the callers are not correctly passed onto the callers. * Otherwise does not change results from previous version.
2.7.0
* Added another feature: consistent/inconsistent calls for paired reads if the position is covered by both forward and reverse reads. However, they're excluded as training features in SomaticSeq.Wrapper.sh script for the time being. * Change non-GCTA characters to N in VarDict.vcf file to make it conform to VCF file specifications.
2.6.1
* Optimized memory for singularity scripts * Updated bamQC.py and added trimSoftClippedReads.py in utilities * Added some dockered scripts at utilities/dockered_pipelines/QC * No change to core SomaticSeq algorithm
2.6.0
* Incorporated TNscope's output VCF into SomaticSeq, although it's not a part of the dockerized somatic mutation workflow.
2.5.2
For paired tumor-normal workflow and bam simulation workflow, singularity-compatible scripts are located at utilities/singularities, with the same commands as dockerized workflows at utilities/dockered_pipelines.