We published the following tools from the GATK 184.108.40.206 and ensembl-vep 109.3 toolkits:
- GATK BaseRecalibrator, which generates a recalibration table based on various covariates for input mapped reads.
- GATK ApplyBQSR, which recalibrates the base quality scores of an input BAM or CRAM file containing reads.
- GATK GatherBQSRReports, which gathers scattered BQSR recalibration reports into a single file.
- GATK HaplotypeCaller, which calls germline SNPs and indels from input BAM file(s) via local re-assembly of haplotypes.
- GATK VariantFiltration, which is used for filtering variants in a VCF file based on INFO and/or FORMAT annotations.
- Augmented Filter VEP, which is a customized wrapper of the filter_vep script from the ensembl-vep toolkit. The tool is modified to allow GNU parallel-scattered filtering of VEP-annotated VCFs split on chromosomes.
- Variant Effect Predictor, which predicts functional effects of genomic variants and is used to annotate VCF files.
In addition, the VEP annotation workflow 109.3 is also live and available in the Public Apps gallery. It is used for preprocessing, annotating, and filtering VCF files using the vt toolkit and VEP.
We also published the PURPLE CNV Calling Workflow used for somatic CNV calling and purity and ploidy estimation on WGS data. It is based on PURPLE 3.7.2, and consists of two additional tools - AMBER and COBALT. The workflow first calculates B-allele frequency (BAF) with AMBER and read depth ratios with COBALT, which is then used by PURPLE to estimate the purity, ploidy and copy number profile of a tumor sample.