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- 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.
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.
- 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.
- 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.
- 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.
- 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.
- 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