PHGv2 Terminology¶

General terms¶

Term	Definition
Reference genome	genome used for initial alignment and base coordinates
Reference range	segment of the reference genome
Haplotype	sequence of part of an individual chromosome with its start and stop defined by the reference range
Reference Haplotype	haplotype from the reference genome
Alternate genome	high quality genomes used to identify alternate haplotypes
Alternate haplotype	haplotype derived from a genome assembly
Composite genome	inferred genome based on its composite set of alternate and reference haplotypes
Haplotype ID	MD5 checksum for the haplotype sequence
Sample	genotype (haploid or diploid or higher), taxon, individual
Path	phased set of haplotype ids through the pangenome graph

File Type	Acronym definition	Usage
`.agc`	Assembled Genomes Compressor	Efficient genome sequence compression.
`.bam`	Binary Alignment Map	Binary representation of a SAM file; useful for efficient processing.
`.bed`	Browser Extensible Data	Genomic feature coordinate (e.g. reference ranges) storage.
`.bcf`	Binary Call Format	Binary representation of a VCF file; useful for efficient processing.
`.fasta`	FAST-All	Sequence representation and storage.
`.g.VCF`	genomic VCF file	Variant and non-variant genomic storage.
`.h.VCF`	haplotype VCF file	Haplotype information representation and storage. More information can be found here.
`.maf`	Multiple Alignment Format	Multiple alignment storage; basis for gVCF and hVCF creation.
`.sam`	Sequence Alignment Map	Sequence alignment to a reference sequence.
`.vcf`	Variant Call Format	Genetic variant representation and storage.

Software	Purpose
agc	Performant FASTA genome compression
AnchorWave	Sensitive aligner for genomes with high sequence diversity
bcftools	Utilities for indexing VCF data
samtools	bgzip compression for VCF data
TileDB	Performant storage core for array data
TileDB-VCF	API for storing and querying VCF data