HaplotypeCaller
We used GATK v4.1 HaplotypeCaller in -ERC mode to generate 107 individual sample g.vcf files for both parent and offspring. Individual g.vcf’s were combined in batches of 20 using CombineGVCFs into a single multiple sample g.vcf comprising the full mixed ploidy cohort. GenotypeGVCF was used to call SNPs on the full cohort. Both commands for combining and genotyping are able to handle mixed ploidy of samples. We used the standard GATK hard-filter expression (https://gatk.broadinstitute.org/hc/en-us/articles/360035532412?id=11097) as our initial filtering step, as P. contorta lacks a benchmark set of high-quality SNPs for calibration and therefore we could not use variant quality score recalibration (VQSR). After the hard-filter expression we filtered out sites with less than 30 quality score, genotype calls with less than 20 genotype quality, and then applied the common set of filters (Table 1).