@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)