Check for VCF sorting

• 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.

Make compatible with .cram

• 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.

minor changes and bug fixes

• 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.

minor improvements

• 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.

maintenance release

• 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

Incorporated TNscope output

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

Added singularity-compatible scripts

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.

minor updates for pipeline scripts

• Additional passable parameters options to pass extra parameters to somatic mutation callers. Fixed a bug where the "two-pass" parameter is not passed onto Scalpel in multiThreads scripts (although I have extensively tested --two-pass parameter and found it to have ZERO effect).
• Ignore Strelka_QSS and Strelka_TQSS for indel training in the SomaticSeq.Wrapper.sh script.

few features and improvements

• Fixed the bug where "CD4" in the output VCF file where alternate concordant reads where grabbed twice, when it should've been alternate concordant and then alternate discordant read.
• Added (limited) tumor-only support.
• Convert VarDict's "Complex" variants into SNVs when appropriate.
• Slightly modified r_scripts/ada_model_builder_ntChange.R script, i.e., the arguments succeeding the input TSV file are features to be ignored in training.

maintenance release

• Updated some docker job scripts.
• Added a script that converts some items in the VCF's INFO field into the sample field, to precipitate the need to merge multiple VCF files into a single multi-sample VCF, i.e., utilities/reformat_VCF2SEQC2.py.
• No change to somaticseq algorithm.