Tetraploid vcf

In total 380 potato clones were genotyped. Library construction and genotyping by genotyping by sequencing (GBS) was outsourced to the Genomics Facility at Cornell University in 2015. The DNA was digested with EcoT221 restriction enzyme and the libraries were 48x multiplexed for sequencing. For polyploid calling the raw FASTQ files were processed with Stacks (Catchen et al., 2013) to remove the barcodes and with TrimGalore https://github.com/FelixKrueger/TrimGalore to trim the ends of reads. The reads were aligned to the reference genome version <i>S. tuberosum_448_v4.03</i> (Sharma et al., 2013) using BWA (Li and Durbin, 2009) and the resulting SAM files were converted to BAM files using Samtools (Li et al., 2009). The variants were called using GATK HaplotypeCaller option (Poplin et al., 2017), disabling the duplicate read filter (this is recommended for GBS data) and joint genotyping using the -ERC GVCF mode.