Recently published apps

We have just updated the content of our public app galleries with new GATK releases:

• GATK Pre-Processing For Variant Discovery 4.2.0.0 workflow is used to prepare data for variant calling analysis. The workflow consists of two major segments: alignment to reference genome and data cleanup operations that correct technical biases. Resulting BAM files are ready for variant calling analysis and can be further processed by other BROAD best practice pipelines, like Generic Germline Short Variant Per-Sample Calling workflow, Somatic CNVs workflow, and Somatic SNVs + INDELs workflow.
• GATK Generic Germline Short Variant Per-Sample Calling 4.2.0.0 workflow that calls germline variants in a WGS sample with GATK HaplotypeCaller, starting from an analysis-ready BAM file.

And six GATK 4.2.0.0 tools:

• GATK GatherBQSRReports tool that gathers scattered BQSR recalibration reports into a single file.
• GATK BaseRecalibrator tool that generates a recalibration table based on various covariates for input mapped read data.
• GATK ApplyBQSR tool that recalibrates the base quality scores of an input BAM or CRAM file containing reads.
• GATK HaplotypeCaller tool for calling germline SNPs and indels from input BAM file(s) via local re-assembly of haplotypes.
• GATK VariantFiltration tool used for filtering variants in a VCF file based on INFO and/or FORMAT annotations.
• GATK MergeVcfs, used for combining multiple variant files.

Marko Marinkovic