Table 1.
List of liftover tools
| Name | Chain file UCSC (hg19/hg38) | Tool built on top of the UCSC liftOver | Webtools | Standalone | Input | Integrity preserve | Limit number of rows | Target assembly continuous |
|---|---|---|---|---|---|---|---|---|
| UCSCliftOver | Yes | https://genome.ucsc.edu/cgi-bin/hgLiftOver | C | BED, GFF/GTF | No | Unlimited | Not continuous | |
| rtracklayer::liftOver | Yes | Yes | R | BED | No | Unlimited | Not continuous | |
| CrossMap | Yes | http://asia.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core | Python | SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF | No | Unlimited | Not continuous | |
| NCBIRemap | No, use NCBI remap alignment | https://www.ncbi.nlm.nih.gov/genome/tools/remap | Perl (API) | BED, GFF/GTF, VCF | Yes | 250.000 rows | Continuous | |
| flo | Yes/Build its own alignment | Yes | Ruby | GFF | No | Unlimited | Not continuous | |
| segment_liftover | Yes | Yes | Python | BED, TSV | Yes | Unlimited | Continuous |