human exome/WGS fastq to gvcf variant calling with GATK4 CWL
Find community-built best practices GATK4 variant calling CWL and/or create one from scratch
Run on several PGP samples using su92l
Put everything in a public project and document it thoroughly.
Do some reporting (Multi-QC) and automated interpretation (CLINVAR annotation with SnpEff?)
Second pipeline using Deep Variant
gVCF output is suitable to feed directly into the Lightning CWL for tiling.
#5 Updated by Sarah Zaranek about 2 months ago
Links to collections with BAMS: