Somaticseq

- InDel_3bp now stands for indel counts within 3 bps of the variant site, instead of exactly 3 bps from the variant site as it was previously (likewise for InDel_2bp).
- Collapse MQ0 (mapping quality of 0) reads supporting reference/variant reads into a single metric of MQ0 reads (i.e., tBAM_MQ0 and nBAM_MQ0). From experience, the number of MQ0 reads is at least equally predictive of false positive calls, rather than distinguishing if those MQ0 reads support reference or variant.
- Obtain SOR (Somatic Odds Ratio) from BAM files instead of VarDict's VCF file.
- Fixed a typo in the SomaticSeq.Wrapper.sh script that did not handle inclusion region correctly.

- Incorporated MuTect2 into SomaticSeq, along with some metrics from MuTect2's output VCF files.
- In the SomaticSeq.Wrapper.sh script, you may use either the original MuTect (--mutect)/ Indelocator (--indelocator) or the new MuTect2 (--mutect2) VCF files. However, if you include both, MuTect2 will take precedence.

*\* Typo in mutect input variable, so the wrapper script did not see mutect even when it was provided.
*\* Used the wrong file name for SSeq_merged.vcf2tsv.py in the script.

Updated the release due to a typo in the wrapper script (i.e., mutect_dir instead of mutect_vcf)

SomaticSeq now handles different variant calls at the same chromosome coordinate. The input VCF file can either have multiple lines of the same coordinate, or have multiple calls in the ALT column separated by a comma (e.g., A,G).
Previously, it assumed one single variant call for each position. If there are multiple ALT calls, only most abundant ALT call was considered.

1) Allow long options (e.g., --mutect | -M ) for the SomaticSeq.Wrapper.sh script. The original script is renamed SomaticSeq.Wrapper.1.sh, which will be removed after we make sure there is no bug in the new script.
2) The VCF files generated will have version number written into the header.