EPITREE project - WGS SNPs Oak

In the EPITREE project (https://www6.inrae.fr/epitree-project/Le-projet-EPITREE) we aim at studying the distribution of methylation sites in 10 oak (Q. petraea) genomes. To do so, we had to discriminate between true C/T SNPs and C>T substitutions caused by bisulfite conversion which can lead to misidentified unmethylated Cs. Thus, we performed a global SNPs detection and considered three SNP calling algorithms: bcfTools , FreeBayes and GATK. In order to accuratly identify polymorphisms in these 10 genomes, we selected SNPs identified by the three calling algorithms. We ended up with 15,727,742 SNPs. These SNPs are placed on the 1408 oak scafflods.