LiftoverIndel

Tool to liftover variants between references in an indel-aware manner. Importantly, this tool identifies variants that overlap a region of the target reference that has an indel relative to the origin reference and incorporates that indel into the lifted variant

Currently in minimal-viable-product mode, but should work for most CHM13/GRCh38 reference liftovers. Please note that

Please note:

• Input variants must be biallelic.
• Output variants should be left-aligned and sorted.
• BCF or VCF files can both be read, but using bcf files allows for a much quicker liftover run. I encourage the conversion of all files, even the reference liftover vcfs, to bcf format for this purpose.
• Output format should be autodetected from the provided output file extension.
• Only genotypes are lifted over; while some of the other info/format fields may be correct, these fields are explicitly not touched during liftover. Some/most non-GT fields will be wrong. If lifting these fields is important to you, please post an issue and I will do my best to add this feature.

pip installation/requirements.txt is not set up, but requirements are:

• pyLiftover
• tqdm
• intervaltree
• cyvcf2
• Bio

Once requirements are installed, simply run the following command:

python3 liftover_indels.py \
    vcf_to_lift.bcf \
    vcf_of_assembly_differences.bcf \ # This file needs to be in target assembly coordinates.
    lifted_over_output.bcf \  #This is stdout by default.
    chainfile.chain \
    target_fasta.fasta

Assembly differences vcf can either be generated by you, or in the CHM13/GRCh38 liftover context it can be obtained from the HPRC AWS bucket.
GRCh38-CHM13 vcf.gz file (GRCh38 coordinates). Use when lifting CHM13 -> GRCh38 coordinates.
CHM13-GRCh38 vcf.gz file(CHM13 coordinates). Use when lifting GRCh38 -> CHM13 coordinates.