LiftoverVcf

Base implementation of GATK LiftoverVcf to convert coordinates for variants provided in vcf format to a different genome build.

  • CWL: gatk_liftover.cwl

hg19/GRCh37 to hg38/GRCh38

We have a custom implementation for the pipeline with an additional pre-processing step to convert coordinates from hg19/GRCh37 to hg38/GRCh38. The pre-processing uses preprocess_liftover.py script to:

  • Check if sample identifiers in the vcf file match a list of expected identifiers
  • Exclude non-standard chromosomes and contigs (e.g., GL000225.1)
  • Format chromosome names by adding chr prefix if missing (i.e., hg19 uses only numbers for the main chromosomes). This is necessary as the chain file coordinates use chr based names for chromosomes.

The lift-over step uses the hg19ToHg38.over.chain.gz chain file (https://cgap-annotations.readthedocs.io/en/latest/liftover_chain_files.html#hg19-grch37-to-hg38-grch38) to map the coordinates between the two builds.

  • CWL: workflow_gatk_liftover.cwl

GATK LiftoverVcf.