* Fixed a bug introduced in v3.0.1 that caused the program to handle .vcf.gz files incorrectly. * Incorporated Platypus into paired mode. * When splitting MuTect2 files into SNV and INDEL, make sure either the ref base or the alt base (but not both) consists of a single base, i.e., discarding complex variants like GCAA>GCT.
3.0.1
Fixed a bug that was introduced in v3.0.0, that did not handle Strelka and LoFreq indel files correctly.
3.0.0
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.