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:

Doha Health Week

Genomic Report Campaign

Jamil Alenbawi1, Yasser A. Al‑Sarraj, Umm‑Kulthum. Umlai1, Ayat Kadhi, Nagham N. Hendi1,

Georges Nemerand Omar M. E. Albagha1

Layla I. Mohammed1, Rozaimi Razali1, Zain Zaki Zakaria, Fatiha M. Benslimane, Farhan Cyprian and Maha Al-Asmakh1,

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Genomic Data Test