2.7 Variant calling
SNPs and INDELs (insertions and deletions) were called as previously
described (Zimpel, 2020) using samtools mpileup (Li, 2011) and VarScan
mpileup2cns (Koboldt et al., 2012) with parameters of minimum read depth
of 7, mapping quality and minimum base quality of 20, and strand bias
filter on, followed by annotation using SnpEff (Cingolani et al., 2012).
INDELs as well as SNPs from repetitive regions (PE/PPE, transposases,
integrases, maturase, phage and repetitive family 13E12 genes) were
removed from the analysis (Zimpel, 2020). Genomes were excluded if the
number of heterogeneous SNPs exceeded 15% of the total number of
detected SNPs in a genome.