AmelHap pilot: filter1 data

Honey bee Apis mellifera drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Being haploid, the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole genome sequence data for 688 drones, including 45 newly sequenced Scottish drones, which collectively represent 13 countries, 7 subspecies and various hybrids strains. After alignment to the reference assembly Amel_Hav3.1, and haploid variant calling, we identified 18.9M variants. Whole-genome sequencing data underpinning the dataset is available from the European Nucleotide Archive (ENA), https://www.ebi.ac.uk/ena, with the project accession codes: PRJEB16533, PRJNA311274, PRJNA363032, PRJNA516678, PRJNA544324, and PRJEB39369. 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 using GATK’s GenomicDBImport and GenotypeGVCFs with --sample-ploidy 1 and a window size of 2.5 Mb. This dataset is the result of applying filters to exclude variants with 'QD<20 || QD>40 || MQ < 50 || SOR >3' in the raw dataset, leaving 16.6M variants. The code used in filtering is outlined here: https://bitbucket.org/scriptBee/hapmap-pilot.

西方蜜蜂（Apis mellifera）的雄蜂通常为单倍体，由未受精卵发育而来，仅继承蜂王的等位基因，而不携带其交配过的多只雄蜂的遗传物质。由于单倍体特性，等位基因的有序组合（即单倍型（haplotype））是已知的，因此雄蜂是极具价值的单倍型研究资源。本研究整合了688只雄蜂的全基因组测序数据，其中包含45个新测序的苏格兰雄蜂，这些样本覆盖13个国家、7个亚种及多种杂交品系。将测序数据比对至参考基因组组装版本Amel_Hav3.1并完成单倍体变异检出后，共鉴定得到1890万个变异位点。支撑本数据集的全基因组测序数据可从欧洲核苷酸档案馆（European Nucleotide Archive, ENA）获取，访问链接为https://www.ebi.ac.uk/ena，对应的项目登录号为：PRJEB16533、PRJNA311274、PRJNA363032、PRJNA516678、PRJNA544324及PRJEB39369。测序读段使用BWA-MEM v0.7.17比对至Amel_HAv3.1参考基因组，通过SAMtools v1.9对读段进行排序，使用GATK v4.0.11.0的MarkDuplicates标记重复读段。每个样本的变异位点通过GATK的HaplotypeCaller检出，采用以下非默认参数：--ERC GVCF、--sample-ploidy 1以及-A AlleleFraction。基于GATK的GenomicDBImport和GenotypeGVCFs工具对所有样本进行联合变异检出，参数设置为--sample-ploidy 1，窗口大小为2.5 Mb。本数据集通过对原始数据进行过滤得到，过滤条件为排除满足‘QD<20 || QD>40 || MQ < 50 || SOR >3’的变异位点，最终保留1660万个变异位点。过滤所用代码可在以下链接获取：https://bitbucket.org/scriptBee/hapmap-pilot。