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Table 2 Precision and recall of our method MSA chic compared to GATK

From: Towards pan-genome read alignment to improve variation calling

Measure GATK 20 50 100
SNV precision 0.992161 0.998585 0.998863 0.998773
SNV recall 0.904897 0.997098 0.998695 0.999072
Indel precision 0.364853 0.996514 0.99731 0.997778
Indel recall 0.0624981 0.982659 0.985723 0.985958