Liftover
Convert positions, intervals and variants between hg19, hg38 and T2T-CHM13.
Want to lift a BED file?
API Usage
curl -X POST "https://api.genebe.net/cloud/api-public/v2/liftover?from=hg19&dest=hg38" \
-H "Content-Type: application/json" \
-d '["chr6-160585140-T-G"]'Input formats
Positions in various formats, use any delimiter you like, you can omit chr:
chr6:160585140 6 160585140 chr6-160585140
Variants in any GeneBe supported format. Be careful with the SPDI format (seq:pos:del:ins, ':' delimited) as it is 0-based! To use standard VCF format, use chr-pos-ref-alt, e.g. chr6-160585140-T-G.
chr6-160585140-T-G chr6:160585140 T>G NM_005577.4(LPA):c.4195A>C(p.Thr1399Pro)
Intervals:
chr6:160585140-160585144 chr6 160585140 160585144
Use one entry per line.
Warnings and errors
Every input gets its own status. Variants are lifted together with their alleles, which are rebuilt against the destination reference. Hover over a warning or error code in the table for details, for example REF_MISMATCH (the reference base differs between the genomes), ALT_EQUALS_DEST_REF, STRAND_FLIPPED, PARTIAL_MATCH or MULTIPLE_MAPPINGS.
About liftover
Liftover is a tool that allows researchers to convert their genomic coordinates from one assembly to another.
The process of liftover involves mapping genomic coordinates from one assembly to another using a reference genome that is common to both assemblies. The reference genome provides a bridge between the two assemblies, allowing the tool to accurately map the genomic coordinates. This is achieved through the use of algorithms that take into account the differences in the genome assemblies, such as variations in the genome structure, insertions, deletions, and other genomic changes.
One of the most common use cases of liftover is when working with human genomes. The two most widely used human genome assemblies are hg19 and hg38 (also known as GRCh37 and GRCh38, respectively). These two assemblies differ in several ways, including the number of contigs, the length of the sequences, and the annotation of genes and other genomic features. As a result, researchers working with older data generated using hg19 may need to convert their data to the newer hg38 assembly to take advantage of the latest findings and knowledge.
The tool present on this page allows for easy conversion between hg19, hg38 and T2T-CHM13 (hs1) coordinates.