Made SomaticSeq extendable as a python library. See docs/Manual.pdf for details.
3.0.0.rc2
* Allow parallel processing through somaticseq_parallel.py. * The wrapper scripts written in bash script (i.e., SomaticSeq.Wrapper.sh and ssSomaticSeq.Wrapper.sh) are replaced by somaticseq/run_somaticseq.py, though they're still kept for backward-compatibility.
2.8.1
Fixed a bug in the ssSomaticSeq.Wrapper.sh script (single-sample mode), where the SNV algorithm weren't looking for SNV VCF files during merging when using utilities/getUniqueVcfPositions.py, causing empty SNV files. For previous commands (invoking --gatk for CombineVariants), the results have never changed.
2.8.0
* The program is now designed to crash if the VCF file(s) are not sorted according to the reference FASTA file. * Output are identical to the previous version, as long as the VCF input files are sorted correctly.
2.7.2
* 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.