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Liftover Chain Files

Resource Location

/labs/SysMedBio/Q/Resources/Genomics/liftover_chains

/Volumes/lab/SysMedBio/Resources/Genomics/liftover_chains

Q:\SysMedBio\Resources\Genomics\liftover_chains

This resource contains coordinate conversion chain files used to translate genomic coordinates between different versions of the human reference genome assembly.

Scientific Context

Reference genome assemblies (e.g., hg18, hg19, hg38) represent consensus sequence maps of the human genome. They are updated periodically to resolve sequencing gaps (such as highly repetitive regions, telomeres, and centromeres), correct structural assembly errors, and better represent genetic diversity.

As reference genome assemblies evolve, the genomic coordinates (chromosome and base-pair positions) of features such as genes, exons, regulatory elements, and single nucleotide polymorphisms (SNPs) change. For example, a variant located at chr1:100,000 in the hg19 assembly might map to chr1:105,200 in hg38.

Re-aligning raw sequencing data (FASTQ) to a new assembly is computationally expensive. Instead, bioinformatics pipelines use tools like UCSC liftOver, CrossMap, or R's rtracklayer to convert coordinate annotations (stored in formats like BED, VCF, GFF, or BigWig) between assemblies using coordinate mapping files called chain files.

What are Liftover Chain Files?

  • Chain Files: Store pairwise alignment maps between a source (query) genome assembly and a target reference assembly. They allow for gaps (insertions and deletions) in both target and query sequences simultaneously.
  • .over.chain.gz files: These represent filtered alignments (net-level chains) that represent the single best, non-overlapping, and highest-scoring mapping. They are specifically optimized for standard coordinate conversion using the UCSC liftOver utility.

Available Files

The directory contains the following coordinate mapping files (downloaded from UCSC GoldenPath):

  • hg18ToHg38.over.chain.gz: Used to lift coordinates from the NCBI36/hg18 assembly (released in 2006) to the GRCh38/hg38 assembly.
  • hg19ToHg38.over.chain.gz: Used to lift coordinates from the GRCh37/hg19 assembly (released in 2009) to the GRCh38/hg38 assembly.
  • hg38ToHg19.over.chain.gz: Used to back-port or lift coordinates from the GRCh38/hg38 assembly (released in 2013) to the GRCh37/hg19 assembly.