Genome Analysis Workflow with Accelerated Variant Calling

Sequencing reads in FASTQ format were generated from Illumina image data using bcl2fastq program (Illumina). Following the OQFE (original quality functional equivalent) protocol^{74 (link)}, sequence reads were mapped to GRCh38 references using BWA MEM^{75 (link)} in an alt-aware manner, read duplicates were marked, and additional per-read tags were added. Single nucleotide variations (SNV) and short insertion and deletions (indels) were identified using a Parabricks accelerated version of DeepVariant v0.10 with a custom WES model and reported in per-sample genome VCF (gVCF)^{76 (link)}. These gVCFs were aggregated with GLnexus v1.4.3^{77 (link)} into joint-genotyped multi-sample project-level VCF (pVCF), which was converted to bed/bim/fam format using PLINK 1.9^{78 (link)} for downstream analyses.

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Sun K.Y., Bai X., Chen S., Bao S., Kapoor M., Zhang C., Backman J., Joseph T., Maxwell E., Mitra G., Gorovits A., Mansfield A., Boutkov B., Gokhale S., Habegger L., Marcketta A., Locke A., Kessler M.D., Sharma D., Staples J., Bovijn J., Gelfman S., Gioia A.D., Rajagopal V., Lopez A., Varela J.R., Alegre J., Berumen J., Tapia-Conyer R., Kuri-Morales P., Torres J., Emberson J., Collins R., Cantor M., Thornton T., Kang H.M., Overton J., Shuldiner A.R., Cremona M.L., Nafde M., Baras A., Abecasis G., Marchini J., Reid J.G., Salerno W, & Balasubramanian S. (2023). A deep catalog of protein-coding variation in 985,830 individuals. bioRxiv.

Publication Preprint 2023

bcl2fastq program

Deletions Genome Indels Joint Nucleotide

Corresponding Organization :

Other organizations : Regeneron (United States), Universidad Nacional Autónoma de México, University of Oxford

Top 5 similar protocols

Variable analysis

independent variables

Sequencing reads in FASTQ format were generated from Illumina image data using bcl2fastq program (Illumina).
Sequence reads were mapped to GRCh38 references using BWA MEM in an alt-aware manner.
Read duplicates were marked, and additional per-read tags were added.
Single nucleotide variations (SNV) and short insertion and deletions (indels) were identified using a Parabricks accelerated version of DeepVariant v0.10 with a custom WES model.

dependent variables

Sequencing reads in FASTQ format
Mapped sequence reads
Identified single nucleotide variations (SNV) and short insertion and deletions (indels)

control variables

GRCh38 reference
BWA MEM mapping method
DeepVariant v0.10 with custom WES model

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