Version 1

Samples that PASS the pre-aggregation QC pipeline (per sample QC) are aggregated into one multi-sample VCF file. Sample are aggregated using Dragen Iterative gVCF genotyper. To accelerate the aggregation and the downstream analyses (parallel processing), the genome is split into 100 shards. 

The output of this pipeline is a multi-sample VCF. One multi-sample VCF is generated per shard in addition to the global multi-sample VCF files (all shards concatenated).