AirLift remaps read alignments between similar reference genomes up to 27.4x faster than full re-mapping while maintaining high accuracy for SNP and INDEL variant calling as validated with GATK.
http://crossmap.sourceforge.net/#use-pip-to-install-crossmap
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AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
AirLift remaps read alignments between similar reference genomes up to 27.4x faster than full re-mapping while maintaining high accuracy for SNP and INDEL variant calling as validated with GATK.