bcbio-nextgen v1.2.4 Release Notes
Release Date: 2020-09-21 // over 3 years ago-
1.2.4 (21 September 2020)
- โ Remove deprecated
--genomicsdb-use-vcf-codec
option as this is now the default. - โ Add bismark output to MultiQC.
- ๐ Fix PS genotype field from octopus to have the correct type.
- ๐ 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
- โ 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. - ๐ 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. - ๐ Allow custom options to be passed to
featureCounts
. - ๐ Fix race condition when running tests.
- โ Add TOPMed as a
datatarget
. - โ Add predicted transcript and peptide output to arriba.
- โ Add mm10 as a supported genome for arriba.
- Skip
bcbioRNASeq
for more than 100 samples. - โ Add
rRNA_pseudogene
as a rRNA biotype. - โ 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. - โก๏ธ update VEP to v100
- โ 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.
- โ Add support for Qiagen's Qiaseq UPX 3' transcriptome kit for DGE. Support for 96 and 384 well configurations
by specifyingumi_type: qiagen-upx-96
orumi_type: qiagen-upx-384
. - โ Add consensus peak counting using featureCounts.
- Skip using autosomal-reference when calling ataqv for mouse/human, as this has a problem with ataqv
๐ (see ParkerLab/ataqv#10) for discussion and followup. - โ Add pre-generated ataqv HTML report to upload directory.
- ๐ Support single-end reads for ATAC-seq.
- ๐ Move featureCount output files to featureCounts directory in project directory.
- โ 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.
- โ Add
kit
parameter for setting options for pipelines via just listing the kit. Currently only implemented for WGBS.
- โ Remove deprecated