Assets 2

Fixed a bug that was introduced in v3.0.0, that did not handle Strelka and LoFreq indel files correctly.

@ltfang-bina ltfang-bina released this Aug 27, 2018 · 7 commits to master since this release

Assets 2

Made SomaticSeq extendable as a python library.
See docs/Manual.pdf for details.

@ltfang-bina ltfang-bina released this Aug 24, 2018 · 8 commits to master since this release

Assets 2
  • 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.

@ltfang-bina ltfang-bina released this Jul 12, 2018 · 97 commits to master since this release

Assets 2

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.

@ltfang-bina ltfang-bina released this Jul 2, 2018 · 124 commits to master since this release

Assets 2
  • 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.

@ltfang-bina ltfang-bina released this May 23, 2018 · 186 commits to master since this release

Assets 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.

@ltfang-bina ltfang-bina released this Mar 28, 2018 · 219 commits to master since this release

Assets 2
  • 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.

@ltfang-bina ltfang-bina released this Dec 11, 2017 · 246 commits to master since this release

Assets 2
  • 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.

@ltfang-bina ltfang-bina released this Nov 26, 2017 · 269 commits to master since this release

Assets 2
  • 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

@ltfang-bina ltfang-bina released this Nov 9, 2017 · 334 commits to master since this release

Assets 2
  • Incorporated TNscope's output VCF into SomaticSeq, although it's not a part of the dockerized somatic mutation workflow.