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Base Quality Score Recalibration (BQSR)

Definition
AI-generated

Base Quality Score Recalibration (BQSR) adjusts per-base quality scores in aligned reads so that reported Phred-scale errors better match empirical mismatch rates, using covariates such as sequencing cycle, dinucleotide context, and read group.

Topics
Sequencing Data Analysis Bioinformatics
Related
Base quality Binary Alignment/Map (BAM) Hard filtering

Why it matters in GWAS

Miscalibrated base qualities distort genotype likelihoods and can shift variant calls and genotype filters at scale; BQSR is a standard preprocessing step before joint calling in many WGS/WES pipelines, distinct from Variant Quality Score Recalibration (VQSR), which operates on variant-level annotations after calling.

Example usage

"Base Quality Score Recalibration (BQSR) was run on deduplicated BAMs with a GRCh38 mask of common SNPs for the recalibration table."

Base quality Binary Alignment/Map (BAM) Hard filtering Phred quality score Variant Calling Variant Quality Score Recalibration (VQSR)
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • DePristo MA, et al. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. https://doi.org/10.1038/ng.806
← Base quality Batch →

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