PRJEB39369 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: PRJEB39369.