Variant Calling QA/QC for Clinical Pipelines — Hands-on

Build robust, auditable variant calling pipelines for clinical genomics. This module covers best practices from FASTQ to signed-off VCFs: pre-processing, caller selection and tuning, artifact mitigation, orthogonal confirmation strategy, and comprehensive validation for regulated settings.

Variant Calling QA/QC for Clinical Pipelines

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Session Index Category 5 · Clinical & Translational Bioinformatics

Session 1 — Pre-processing & Read-Level QC Session 2 — SNV/Indel Calling & Filtering Session 3 — CNV/SV & Fusion Detection Session 4 — Validation, LoD & Audit Readiness

Session 1

Fee: Rs 13520

Pre-processing & Read-Level QC

Alignment and pre-processing

BWA MEM2 mark duplicates & UMI BQSR

Run metrics & artifacts

coverage & uniformity on target & duplication FFPE & oxidative lesions

Contamination & mixture

PON & cross sample checks sex & fingerprint concordance tumor purity notes

Session 2

Fee: Rs 17720

SNV/Indel Calling & Filtering

Callers and tuning

GATK HaplotypeCaller & Mutect2 Strelka2 & VarDict panel of normals

Filtering & annotation

hard vs model filters VEP & snpEff artifact blacklists

TMB/MSI & signatures overview

coverage constraints reporting thresholds orthogonal checks

Session 3

Fee: Rs 21920

CNV/SV & Fusion Detection

CNV calling strategies

CNVkit & ExomeDepth panel normalization QC of exons & genes

SVs and fusions

Manta & GRIDSS RNA fusions overview breakpoint confirmation

UMI and low VAF design

error suppression duplex logic reportable range

Session 4

Fee: Rs 27520

Validation, LoD & Audit Readiness

Truth sets & orthogonal confirmation

GIAB & NA12878 ddPCR/Sanger reference materials

Analytical validation studies

LoD & reportable range sensitivity/specificity/PPV precision & reproducibility

SOPs, change control & documentation

traceability & audit trails Snakemake/Nextflow runners release packages

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Variant Calling QA/QC for Clinical Pipelines | SNV/Indel, CNV/SV, Validation & Compliance

Variant Calling QA/QC for Clinical Pipelines — Hands-on