PRJNA311274 gVCFs part 1

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. This dataset comprises the gVCF files for a subset of samples belonging to project accession: PRJNA311274.

使用BWA-MEM v0.7.17软件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。使用GATK的单倍型调用器（HaplotypeCaller）对每个样本进行变异检测，设置如下非默认参数：--ERC GVCF、--sample-ploidy 1 及 -A AlleleFraction。本数据集包含隶属于项目登录号PRJNA311274的部分样本的基因组变异调用格式文件（gVCF）。