Cannabis SNPs called from whole genome sequencing data.

SNPs called from WGS data of 27 cannabis accession, 12 auto-flowering and 17 photoperiod sensitive. Data is for chromosome 5 only, Purple Kush assembly (ASM23057v4). Annotated as chromosome 1 in other assemblies.
Methods:
Comparative population genetics statistics for chromosome 5 (Purple Kush assembly ASM23057v4) were performed using WGS data from 17 photoperiod-sensitive and 12 auto-flowering genotypes. Genome Analysis Toolkit (GATK) was used for variant calling (McKenna et al., 2010). VCFtools v.0.1.16 (Danecek et al., 2011) was used to filter biallelic SNPs and remove SNPs with minor allele frequencies <1% and missing data >20%. After filtering, 916 000 SNPs on chromosome 5 were used for downstream analyses.
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A. et al. (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303. Available from: https://doi.org/10.1101/gr.107524.110
Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A. et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156–2158. Available from: https://doi.org/10.1093/bioinformatics/btr330