4.0.2 (GATK4 pipeline)

• updated all tool versions for running on gearshift

3.5.5 (Uakari)

• replaced hard filter FS for SOR

  • for indels: "FS > 200.0" is now "SOR > 10.0"
  • for snps: "FS > 60.0" is now "SOR > 3.0"

• added fastQ information to the header of the vcf

• added gendercheck information to resultsfolder (was not in resultsfolder before)

3.5.4 (Tiger)

updates:

• requesting resources for a protocol is now handled via a parameters file (bigger datasets sometimes require more resources). all #MOLGENIS headers are removed from the protocols. This can now be used with the new Molgenis-Compute (see below)

• reads with a mapping quality below 20 will not be used in calculating coverage

• new Molgenis-Compute-19.01.1-Java-11.0.2 version (before: Molgenis-Compute-17.08.1-Java-1.8.0_74)

bugfixes:

• (diagnostics) fixing ONCO_v5 issue. The pipeline will execute genderCheck automatically when there is chrX available. ONCO_v5 has only a very small percentage of targets on chrX which is not reliable enough. fix: when ONCO, no GenderCheck
• rejected samples (due to no or 0.0% reads for a barcode) were not removed from the samplesheet.
• Gavin bugfix: when choosing option BOTH the merged INFO fields will be pasted directly to the other INFO fields without a separator, this is now fixed (with perl replace command)

3.5.3 (Scorpion)

• Documentation updates
• Fix in copying the vcf files for the concordance check

3.5.2 (Rhino)

• added GavinStandAlone to the NGS_DNA repo
• updated docs
• tiny bugs in the dependencies in the workflow
• bugfix in GenderCalculate, when there is noChrX it will produces an error due to missing initialisation of a variable
• Gavin output will be outputted in compressed format due to issues with downstream analysis

3.5.1 (Quetzal)

MAJOR BUGFIX

MarkDuplicates: lanes from same sample are merged instead of per lane

new:

• first version of CartegeniaTree (NOT IN USE by diagnostics)

• Determine trio's (using VCFped, https://github.com/magnusdv/VCFped)

• using vcfanno for annotation of the variants (https://github.com/brentp/vcfanno/releases) (Field names are between round brackets)

  • CADD (CADD_SCALED, CADD)
  • ExAC (EXAC_AF, EXAC_AC_HET, EXAC_AC_HOM)
  • gnomAD gnomAD_Hom, gnomAD_Hemi, gnomAD_AN, gnomAD_exome_AF_MAX, gnomAD_exome_RF_Filter,EXAC_AF)
  • CGD CGD_Condition, CGD_Inheritance, CGD_AgeGroup, CGD_Manfest_cat, CGD_invent_cat, invent_rat)
  • GoNL (GoNL_AC, GoNL_AN)
  • Clinvar (clinvar_dn, clinvar_isdb, clinvar_hgvs, clinvar_sig)

• new version of GAVIN (https://github.com/molgenis/gavin-plus/releases)

  • CGD_26jun2018.txt.gz
  • clinvar.vkgl.patho.26june2018.vcf.gz
  • FDR_allGenes_r1.2.tsv
  • GAVIN_calibrations_r0.5.tsv

updated tools

• SnpEff/4.3t-Java-1.8.0_74
• multiqc/1.6
• gavin-plus/1.5.0-Java-1.8.0_74
• ngs-utils/18.06.2
• BCFtools/1.6-foss-2015b

new tools:

vcfanno/v0.2.9

updates:

• created folder that can be picked up by ChronQC for long time statistics
• removing rejected samples out of samplesheet ( if samples will be rejected this will be mailed to mailing group)
• added cram index file
• added single read functionality
• some data will be moved directly to resultsfolder (bam,cram,fastqc,gVCF)

3.4.4 (Pelican)

updated

• docs
• changed prm/cluster for diagnostics
• decreased resources used in some protocols
• removed unused workflows (gonl/hmf)
• removed crashing the pipeline on the genderCheck, now instead it will drop an email and the gender that is calculated will be the "truth" while continuining the pipeline
• added coverage check, when more than 10% of the targets are below 20x coverage, the sample will be rejected (writing to ${sampleNameID}.rejected )
• added check if bedfile exists

bugfixes

• CopyToResultsDir: copying rejectedSamples => misplaced quote
• removed FIFO pipe in prepareFastQ step since this sometimes occurs in an error

3.4.3 (Okapi)

Added:

• GeneNetwork annotation step

• new QCReport (MultiQC)

• MantaAnnotation

• included track and trace in header and footer

• panels and exomes can now be in one project

• fixing phiX concordance check

3.4.2 (Nightingale)

• Updated data staging prm->tmp in NGS_DNA and removed this from NGS_Automated.

• updated test (is now testing for both external_samples as in-house samples)

• added startFromVcf part to the pipeline

NGS_DNA 3.4.1 (Mandrill)

• created trackNtrace header/footer + removal of cutadapt in PrepareFastQ
• fix for not having a vcf index issue
• removing EBROOTSAMBAMBA since it is added to the PATH
• added gender check alarm when samplesheet says e.g. Male and calculated gender is Female
• changing output in PrepareFastQ step since it has storage issues when deploying multiple big jobs
• added M&M part to QCReport
• added set -eu to first rocket
• changed generate_template (it will now work with named arguments)