Feature gears (metagenomics)

Metagenomics pipeline, start from bam or from FastQ files.

Dependencies:
- Sambamba (v0.5.1+)
- Kraken

See merge request !168

Feature yamsvp

Merging into develop to change the extensions/tools section

keep yamsvp branch for development!

See merge request !122

Update code to v0.4 branch and fix usage of Ln and memory settings of VMEM, settings for memory will be committed to the shark-config branch with recommended defaults.

Feature reference

Part of issue #81

This is only checking and not auto generating anything. Adding auto generate is now not a lot of work anymore.

See merge request !147

add more info to VepNormalizer tool help

self-explanatory.

See merge request !157

Feature vcfanotate

Adding a feature for project

See merge request !167

shift option had wrong var name

See merge request !155

Show all lines that do not belong to a stacktrace now

See merge request !166

Patch picard summary

changing some summaries for picard metrics

See merge request !163

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

Feature vcffilter trio filters

Added some more filter options

See merge request !162