Version 1 (25k release)

Changelog

• Lossless CRAM replaces the BAM format for reads alignement files
• Sample IDs in CRAM and VCF files are updated to keep only the QPHI unique ID 
• New Individual and cohort-level Quality Control (QC) steps introduced in the QGP Pre-Aggregation QC pipeline V1, to remove samples with sequencing issues
• New file formats are delivered for each release (Plink, Hail, PCs, Relatedness, etc.)
• New variants callers (SV, CNV, PGx, SMN, HLA, STRs, etc.

Version 1.0

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

Version 1

Each WGS sample is tested independently through this pipeline. If a sample fails the test, it is excluded from the aggregation process and will not be included in the final release. These tests are designed to identify sample swaps, cross-individual contamination, and errors in sample preparation or sequencing. A detailed list of specific QC processes is provided in the table below:

Version 1

Genomic raw data is processed using the Dragen solution.

 All callers from the Dragen DNA pipeline are activated.

This pipeline takes two types of input files: