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bcbio-nextgen v1.1.2 Release Notes

Release Date: 2018-12-12 // over 5 years ago
    • VarDict low frequency somatic filters: generalize strand and mismatch based filter based on cross-validation to avoid over filtering on high depth panels.
    • strelka2 joint calling: switch to improved gvcfgenotyper approach for calling from gVCFs.
    • 👍 Heterogeneity: initial support for PureCN and TitanCNA heterogeneity analysis including reporting on LOH in HLA for human samples. Work in progress validations: https://github.com/bcbio/bcbio_validations/tree/master/TCGA-heterogeneity
    • 👍 CNV: initial support for GATK4 CNV calling as alternative to CNVkit for tumor normal analyses
    • VarDict RNA-seq variant calling: avoid structural variants with recent vardict-java.
    • RNA-seq variation: filter RNA-seq variants close to splice junctions, supporting STAR and hisat2.
    • RNA-seq variation: add snpEff effects to output variant calls. Thanks to Manasa Surakala.
    • RNA-seq: gzip/bgzip FASTQ files in work/fastq instead of the original directory.
    • 👉 use biobambam2 BAM to FASTQ conversion instead of Picard in all cases.
    • 👍 Trimming: add built-in support for adapters from the SMARTer Universal Low Input RNA Kit (truseq2) and the Illumina NEXTera DNA prep kit from NEB (nextera2).
    • ChIP/ATAC-seq: allow skipping duplicate marking.
    • joint calling: ensure correct upload to final directory when no annotations present
    • 👷 Logging: fix logging in parallel runs with new joblib loky backend. Thanks to Ben Liesfeld and Roland Ewald.