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@roryk roryk released this 21 Sep 19:34
· 323 commits to master since this release
v1.2.4
aff0de6

1.2.4 (21 September 2020)

  • Remove deprecated --genomicsdb-use-vcf-codec option as this is now the default.
  • Add bismark output to MultiQC.
  • Fix PS genotype field from octopus to have the correct type.
  • Edit VarDict headers to report VCFv4.2, since htsjdk does not fully support VCFv4.3 yet.
  • Attempt to speed up bismark by implementing the parallelization strategy suggested here: FelixKrueger/Bismark#96
  • Add --enumerate option to OptiType to report the top 10 calls and scores, to make it easier to decide how confident we are in
    a HLA call.
  • Performance improvements when HLA calling during panel sequencing. This skips running bwa-kit during the initial
    mapping for consensus UMI detection, greatly speeding up panel sequencing runs.
  • Allow custom options to be passed to featureCounts.
  • Fix race condition when running tests.
  • Add TOPMed as a datatarget.
  • Add predicted transcript and peptide output to arriba.
  • Add mm10 as a supported genome for arriba.
  • Skip bcbioRNASeq for more than 100 samples.
  • Add rRNA_pseudogene as a rRNA biotype.
  • Add --genomicsdb-use-vcf-codec when running GenotypeGVCF. See https://gatk.broadinstitute.org/hc/en-us/articles/360040509751- GenotypeGVCFs#--genomicsdb-use-vcf-codec for
    a discussion. Thanks to @amizeranschi for finding the issue and posting the solution.
  • update VEP to v100
  • Add consensus peak calling using https://bedops.readthedocs.io/en/latest/content/usage-examples/master-list.html
    to collapse overlapping peaks.
  • Pre-filter consensus peaks by removing peaks with FDR > 0.05 before performing consensus peak calling.
  • Add support for Qiagen's Qiaseq UPX 3' transcriptome kit for DGE. Support for 96 and 384 well configurations
    by specifying umi_type: qiagen-upx-96 or umi_type: qiagen-upx-384.
  • Add consensus peak counting using featureCounts.
  • Skip using autosomal-reference when calling ataqv for mouse/human, as this has a problem with ataqv
    (see ParkerLab/ataqv#10) for discussion and followup.
  • Add pre-generated ataqv HTML report to upload directory.
  • Support single-end reads for ATAC-seq.
  • Move featureCount output files to featureCounts directory in project directory.
  • Remove RNA and reads in peak stats from MultiQC table when they are not calculated for a pipeline.
  • Only show somatic variant counts in the general stats table, if germline variants are calculated.
  • Add kit parameter for setting options for pipelines via just listing the kit. Currently only implemented for WGBS.
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