We established an indexed EMS mutant library for the wheat cultivar KN9204, which is cultivated in northern China. To identify genetic mutation caused by EMS, targeted exome-capture sequencing was performed using probes specifically designed for the KN9204 genome (Wang et al., 2023 Plant Communications). Raw variant call format (VCF) files were obtained for 1,839 mutant lines through SNP detection using the Genome Analysis Toolkit (GATK) best practices workflow, encompassing the complete variant calling pipeline from raw read processing to final variant filtration. Primary variant filtration was performed using BCFtools with stringent quality thresholds (%QUAL < 50 || INFO/DP < 5), followed by the removal of SNPs exhibiting mutation frequencies exceeding 0.7%. This two-step filtration strategy yielded a refined VCF file containing high-confidence variants for downstream analyses.