Changed IC_db_template to allow relative path
Enabled slurm script again for VMERGE
Merge branch 'feature/intersectcollect_from_diff_projects' into develop
Use of Annovar db & changed IC_template out info

- Removed hard coding of db used with Annovar. Instead user can supply a comma separated list of Annovar table names to use in the Annovar annotation.
- Added flag to list MIP supported Annovar db:s.
- Changed header and column info in IntersectCollect template after VMERGE to e.g. "outinfo:chr=>0_0,Start=>0_1 format" for readability. IntersectCollect stills supports outcolumns and outheaders format, but outinfo has been added.
- Added flag for maximum number of cores per node used in the MIP.
Parameter changes, Pedigree support, sanity check of files

- Renamed and syntaxed parameters
- Added environment variable 'env_up' for running with standard settings on uppmax
- Added support to read pedigree files
- Added automatic defaults when using the 'env_up' flag. Standard analysis can now be inititated using only "mip_align.pl -p b2010080 -familyid 33 -env_up 1".
- Added support for different capture files between samples when using pedigree to supply info.
- Added sanity check for files needed by each program. Run will terminate if file(s) is lacking.
- Added complete cmd line recreation to master_logg, enabling instance modifications before rerun.
Select variants for DbIEM

- Use ensembleGeneID for selecting variants found in dbIEM. Overlapping genes with ensembleGeneID not found in dbIEM will be printed to orphan file. A hit in dbIEM and another geneID which does not belong in the DbIEM will be printed to both orphan and dbIEM.
- Added new feature to intersectCollect to enable selection of variants given Db files.
Merge branch 'release/v0.1.0'
Capture kit from Pedigree file

- Added support for Agilent SureSelect V2-5.
- Version of capture kit .bed, infile_list and padded infile_list is automatically collected from reference genome supplied when using 'env_up' flag and not supplying a pedigree file.
Added support for configuration files (YAML), fixed missing last target in coverage report, changed format of GT call

- MIP can now handle configuration files (YAML). Requires perl YAML.pm installation. Precendence: 1. cmd line 2. Config file 3. EnvironmentUppmax
- Last target region is now included in coverage report
- Format of GT call changed to provide a cleaner and more easily parsable entry.
Dry run capabiblites, clearer syntax, noback-up used by default

- Added dry run capabiblites. When enabled process everything, but do not submitt to SLURM.
- Made substantial changes to syntax
- All data files will be written to nobackup when using '-env_up'
- Automatic removal of picardToolsMerge TMP_DIR.
Introduce mip.pl, decomission mip_align.pl and mip_variation.pl

- MIP is now a single script (mip.pl)
- Improved parameter handling through subroutines
- Improved subroutine for sbatch submission. Can now handle extended forks
- GATK realign and base recalibration is now done on original BAM and not split per chr due to the parallelization option added by GATK
- Cleanup of code and parameters
- IntersectCollect template now dynamically handles fileendings
- changed "-p node" to "-p core" where relevant to accomodate UppMax changes
Deleted temp files
TMP directory

- Changed picardTools & GATK TMP directory default to stub and added the SLURM jobID as suffix.
Minor changes

- Removed ".." error
- Changed default settings for $aligner
GATK - Minor changes

- Allocated more memory for java heap to accomodate single BAM-file use in realignment and base recalibration
Validated realignment and base recalibration
Updated README and included unvalidated GATK phasing
Submission paths, added BWA Mem

- Changed submission path to MAIN dowstream of haplotyper
- Added BWA Mem support
Added -prechr to rank script, changed default dbIEM geneId column

- Added chromosome prefix to rank script to accomodate different references
- Changed default ensemblgeneID columnin dbIEM to match version 1.1.
Merge branch 'release/v1.1'