Integrated multi-omics analysis dissects fruit quality traits and establishes a robust genomic selection platform in Chinese cherry (Prunus pseudocerasus Lindl.)

Genotypic data (multi-sample vcf) of Prunus pseudocerasus Lindl, in association with the paper 'Integrated multi-omics analysis dissects fruit quality traits and establishes a robust genomic selection platform in Chinese cherry (Prunus pseudocerasus Lindl.)'. Variant calling followed the GATK (v4.5.0) best practices pipeline. Base Quality Score Recalibration (BQSR) was performed using a high-confidence variant set derived from an initial round of calling. HaplotypeCaller was then used to generate GVCF files for each individual with the ploidy set to 4 (-ploidy 4). Joint genotyping was performed using GenotypeGVCFs to produce a raw multi-sample VCF.