v1.4.0 - Kingly Kortrijk

New Features

1. Added the --callers parameter to specify the variant caller to use. Currently only haplotypecaller and vardict are supported.
2. Added the vardict variant caller.
3. Added the --vardict_min_af parameter to specify the minimum allele frequency for vardict. This option is also available in the samplesheet as vardict_min_af to set it dynamically per sample.
4. Added the --output_genomicsdb option to specify whether a GenomicsDB should be outputted or not. This will be true when using only_merge.
5. Added --normalize options for decomposing and normalizing of variants after calling and genotyping.
6. Added WGS, WES, SeqCap, HyperCap and seqplorer profiles that can be used to set the default parameters for these types of runs.

Improvements

1. Refactored the pipeline to accomodate future additions of variant callers and genotypers
2. Removed a lot of unnecessary bloat
3. Improved GenomicsDBImport (can now be multithreaded and runs a lot faster). This will make very big runs more possible.
4. Changed coverage_fast to mosdepth_slow, reversing the effect of the parameter. By default mosdepth will now be run with --fast-mode. This can be disabled using the new mosdepth_slow parameter.
5. Automatically merge the regions that are within 150 bps of eachother for the variant calling. This way it's ensured that indel calling happens correctly.

Fixes

1. Fixed an issue with the outputting of the validation PNG files, now all three types of PNGs are outputted.
2. Fixed a small issue where VCFs without a sample created by the callers could not be used by bcftools concat, these files will now be filtered from the input of the command.
3. Removed the --maxentscan parameter because this file is automatically present in the container