Make BQSR variants optional
Rationale
In order to make hutspot more general, the hard coded requirement to specify three different known SNP databases should be removed. Instead, there should be an option to specify 0 or more files which contain knowns SNPs to be used to perform BQSR. If no files are specified, the BQSR step should be skipped.
The arguments to be removed are:
- DBSNP
- ONETHOUSAND
- HAPMAP
The argument to be added:
KNOWN_SITES
which can be 0 or more vcf files. If all three variant files listed above are specified, the behaviour of the pipeline should not change.
ANNOTATE_VARIANTS
This is the database to be used to annotated the variants that were found. To preserve the default behaviour, this should be the DBSNP file. This way, it is made explicit which vcf files are used for BQSR, and which are used to annotate the variants.