Variant Catalogs
Alignment and variant calling pipelines frequently depend on reference variant catalogs. These catalogs contain known variant sites, such as polymorphic sites for single nucleotides, insertions, or deletions, providing information about genetic variation that improves the accuracy of the models used in variant calling.
The pipelines utilize several of these catalogs, specifically the versions built using the GRCh38 Genome Build.
Catalogs
- The Single Nucleotide Polymorphism Database: A comprehensive repository documenting single nucleotide changes in genomic DNA.
- Mills and 1000 Genomes Gold Standard: A comprehensive catalog documenting insertions and deletions in genomic DNA.
- gnomAD Population Allele Frequencies for Mutect2: gnomAD population allele frequencies for Mutect2 (GATK Best Practice).
- Brain Somatic Mosaicism Network Panel of Normals: A collection of variants observed across multiple unrelated samples generated by the Brain Somatic Mosaicism Network as a panel of normals.