CrossMap: a versatile tool for coordinate conversion between genome assemblies

By Hao Zhao, Zhi-fu Sun, Jing Wang, Haojie Huang, Jean-Pierre A. Kocher, Liguo Wang. 2014

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High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios (2021, methodology): “This was done by going over each interval in GRCh38 GIAB confident regions and trying liftover to GRCh37 using CrossMap 44 .”
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, methodology): “0 (43), (ii) CrossMap (41) and (iii) Cytoscape 3.”
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, methodology): “In addition we create chain format files of our assembly version mappings to be used by liftover (31) or CrossMap (32).”
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies (2017, methodology): “For usage with the PacBio, 10X Genomics, and Rao Hi-C data, the hg18 NA12878 VCF file was carried over to hg19 with CrossMap (Zhao et al. 2014).”