SNP_variant_calls_using_KSSc38901_transcriptome_reference_for_alignment

Prior to calling SNPs between parents, the raw transcriptome sequence reads of each parent were aligned against reference sequences. Initial alignment of raw sequences from KSSc38901 and GKP10017 for identification of SNPs. Raw sequences of GKP10017 and KSSc38901 were aligned against the KSSc38901 transcriptome (Chopra et al. 2014) and A. duranensis V14617 genome sequences (Bertioli et al. 2016) using the bwa.0.7.5a (Li and Durbin, 2009) aligner with the backtrack approach. After alignment of the raw reads of KSSc38901 and GKP10017, the GATK version 2.6 variant calling tool (DePristo et al. 2011) was used to identify SNPs and InDels between these genotypes using the default parameters for UnifiedGenotyper and ploidy level of 2. Parameters of “Quality Depth (QD) < 10.0 || Mapping Quality < 40.0 || Allele Frequency < 0.25 || Read Depth (DP) < 40” were used to filter the SNP calls using vcftools version 1.1 (Danecek et al. 2011). Variant statistics were calculated using the vcf-stats script from vcftools version 1.1 (Danecek et al. 2011).