Feature vcfstats

Adding new functions to vcf stats:
* [x] improved sample allele overlap
* [x] report bin stats in wiggle tracks
* [x] adding sample distribution files

See merge request !134

Patch varscan

This pull request fixes an error caused by incorrect passing of the Java flags to the VarScan command used in Gentrap. For local runs, it has no effect. However, these are important for cluster runs.

See merge request !137

Patch flexiprep

found bug in flexiprep, seqstat can't find fastq when input fastq (extracted by zcat) is removed because only input is the link file from seqtk.

Is this hot fix worthy? I not sure but it could be a blocking bug.

See merge request !136

Patch main docs

The main `README.md` file looks obsolete now. This pull request uses the `index.md` we had in the `docs` folder previously as the main `README.md` file. The `docs/index.md` file is now simply a symlink to the root `README.md`

See merge request !135