@RoanKanninga RoanKanninga released this Jan 21, 2019

Assets 2
  • Documentation updates
  • Fix in copying the vcf files for the concordance check

@RoanKanninga RoanKanninga released this Dec 19, 2018 · 27 commits to master since this release

Assets 2
  • 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

@RoanKanninga RoanKanninga released this Nov 23, 2018 · 58 commits to master since this release

Assets 2

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)

@RoanKanninga RoanKanninga released this Mar 26, 2018 · 212 commits to master since this release

Assets 2

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

@RoanKanninga RoanKanninga released this Dec 19, 2017 · 253 commits to master since this release

Assets 2

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

@RoanKanninga RoanKanninga released this Sep 8, 2017 · 342 commits to master since this release

Assets 2
  • 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

@RoanKanninga RoanKanninga released this Jul 27, 2017 · 428 commits to master since this release

Assets 2
  • 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)

@RoanKanninga RoanKanninga released this Jun 12, 2017 · 506 commits to master since this release

Assets 2

GoNL part

Final version GoNL pipeline on b38, reference genome is ucsc build 38 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

new protocols

  • combine TrimAdapters, SpikePhiX and CheckIlluminaEncoding in one protocol (PrepareFastQ.sh)

new files

  • generate_template_gonl.sh
  • workflow_gonl.csv
  • batch_b38_chr.csv
  • workflow_gonl_validating.sh (2 rounds of FastQC and MarkDuplicates)

Version updates

  • dbSNP version 149 (All_20161122.vcf.gz)

Regular pipeline updates

Version updates

  • GATK 3.6 --> 3.7
  • picard 1.130 --> 2.9
  • FastQC 0.11.3 --> 0.11.5
  • BWA 0.7.12 --> 0.7.15
  • sambamba v0.6.4 -> v0.6.6

New tools

  • Using SeqTk (1.2) for the converting the fastQ files from Illumina 1.5 to 1.9 encoding

bugfixes + updates

  • for chr Y ploidy set to 1 (instead of 2)
  • added newQual argument in VariantCalling (see https://software.broadinstitute.org/gatk/blog?id=8692)
  • removed VariantAnnotator out of workflow: HaplotypeCaller can change the bam by the internally indel realignment and VariantAnnotator is updating the genotypes based on the dedup.bam, this is basically not what we want
  • added summary metrics file in GCbias metrics
  • removed stand_call_conf 10.0 in genotyping step, default is 10.0
  • removed stand_emit_conf 20.0 in genotyping step, deprecated in GATK 3.7
  • combine Bwa align with SortBam (by FIFO piping) in one step
  • combine SpikePhiX and CheckIlluminaEncoding in one protocol (PrepareFastQ.sh)

@RoanKanninga RoanKanninga released this Mar 30, 2017 · 628 commits to master since this release

Assets 2

Regular pipeline

  • Gavin output name is smaller
  • Fill in complete path to external samples in samplesheet when running external samples

GoNL first version

  • gonl workflow
  • gonl parameters file

new protocols:

TrimAdapters Trimming of Illumina adapter
BaseRecalibrator prepare BQSR step
Base Quality Score Recalibration rescoring base qualities
VerifyBamID Check if the bam not is contanimated or that there was a sample swap
PhaseByTransmission Trio aware phasing

@RoanKanninga RoanKanninga released this Mar 3, 2017 · 661 commits to master since this release

Assets 2

HMF workflow implementation