SNP Calling Using GATK

Flashcards for key terminology related to SNP calling using GATK.

GATK

Genome Analysis ToolKit, a software used to analyze variation in high-throughput sequencing data.

SNP

Single Nucleotide Polymorphism, a variation at a single position in DNA among individuals.

Indel

Insertion or deletion of bases in the genome.

Reference Genome

A digital nucleic acid sequence database used as a reference for mapping sequences.

Base Quality Score Recalibration

Process to adjust the quality scores of bases in sequencing data.

Joint Calling

The process of calling genotypes from multiple samples together to improve accuracy.

VCF

Variant Call Format, a file format for storing gene variant information.

GVCF

Genomic VCF, a format that contains variant calls and quality information.

Best Practices

A set of standardized workflows to ensure accurate and reproducible results in genomic analysis.

Mark Duplicates

A process of identifying duplicated reads in sequencing data, which should be ignored in analysis.