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@RoanKanninga RoanKanninga released this Apr 8, 2021

  • gender specific result folders for coverage calculations (results/coverageCoveragePer{Base,Target}/{male,female,unknown})
  • small fixes for wgs data
  • bugfixes in curl response for track and trace database

updated

  • gnomAD 2.1.1 (was 2.0.2) (some fields had a name change)
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@Gerbenvandervries Gerbenvandervries released this May 1, 2020

GATK 4 pipeline

NGS_DNA/4.0.3

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@RoanKanninga RoanKanninga released this Feb 13, 2020

bugfixes:

  • number of rows in samplesheet > 200 is not producing an error anymore
  • XT-HS bugfix in CoverageCalculations
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@RoanKanninga RoanKanninga released this Oct 31, 2019

Merge pull request #261 from TDMedina/release_version

WIP updates to the WES pipeline in preparation for future Gearshift deployment.
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@RoanKanninga RoanKanninga released this Nov 25, 2019

  • updated all tool versions for running on gearshift
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@RoanKanninga RoanKanninga released this Sep 23, 2019

  • 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)

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@RoanKanninga RoanKanninga released this Apr 10, 2019

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)
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@RoanKanninga RoanKanninga released this Jan 29, 2019

  • Documentation updates
  • Fix in copying the vcf files for the concordance check
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@RoanKanninga RoanKanninga released this Dec 19, 2018

  • 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
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@RoanKanninga RoanKanninga released this Nov 23, 2018

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)
Assets 2