PRJNA516678 raw variants

Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. Joint variant calling was performed across all samples collated for AmelHap using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 10 Mb. This dataset comprises the raw variant calls only for samples belonging to project accession: PRJNA516678.使用BWA-MEM v0.7.17工具将测序读段比对至西方蜜蜂参考基因组Amel_HAv3.1。随后采用SAMtools v1.9对读段进行排序，并借助GATK v4.0.11.0的MarkDuplicates工具标记重复序列。针对每个样本的变异检出，使用GATK的单倍型调用器（HaplotypeCaller）完成，设置如下非默认参数：--ERC GVCF、--sample-ploidy 1 与 -A AlleleFraction。针对为AmelHap项目整合的全部样本，通过GATK的GenomicDBImport与GenotypeGVCFs工具开展联合变异检出，设置参数为--sample-ploidy 1，窗口大小为10 Mb。本数据集仅包含隶属于项目登录号PRJNA516678的样本的原始变异检出结果。