DNA pipeline 3.1.0 (Bison)

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• Added Delly to pipeline
• Major bug fix in Sex chromosome calling

DNA pipeline 3.0.2 (Armadillo)

Put quotes around variables in comparisons

DNA pipeline 3.0.1 (Armadillo)

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Pipeline is in principle the same as 2.1.2.

Major change:
Pipeline is now ready to work with Slurm and can be used in the new environment (calculon,zinc-finger etc).

• changed parameter file + generate template
• updated tool versions

Small fixes/changes:

• updated batchsize (batches were too big and with gVCF the need for a big batch size is not necessary)
• added environment specific parameter files
• fixed CopyToResults dir bug (.finished file was written on the wrong place)

NGS_DNA-2.1.2 pipeline

Implemented gVCF variant calling + minor bugfixes

DNA pipeline 2.1.1

Big changes has been made, most important change is that VariantCalling. VariantCalling will now be done per project instead of per sample.

new protocols:

• Sequenom concordance check
• CheckSex (there is a check whether a sample is male or female)
• PhiX virus reads are added to each sample. This is done to check if the pipeline ran correctly.
• CoveragePerBase (This is a request of the Diagnostics department). This will only be done on targeted panels and SSID kit samples.

updates:

• VariantCalling is now per project instead of per sample. It is now better visible in the vcf's whether a SNP/Indel was of bad quality or it is homozygous reference call
• ChrParameters is now replaced by batching (50, 200 or 500 batches). This will decrease the running time of the VariantCalling

DNA pipeline 2.0.1

bugfixes to

• loading correct molgenis version in CreateInhouseProjects.sh
• removed unused pindelOutputVcf variable
• changed name of file (without the chr)

DNA pipeline 2.0

Merge pull request #196 from Gerbenvandervries/master

added README.txt, and clean protocols for versionNumber and allOutputExi...

gpfs-pipelines

pipelines suitable for old gpfs structure