CNP0001986 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 2 and -A AlleleFraction. This dataset comprises the gVCF files for a subset of diploid samples from Chen et al. (2022), belonging to project accession: CNP0001986.

Parejo, M., Talenti, A., Richardson, M., Vignal, A., Barnett, M., & Wragg, D. (2022). CNP0001986 gVCFs part 1 (1.1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6806115