I am trialing discoSNP++ as part of a bacterial GWAS pipeline and am seeking some clarification on the genotypes in the multisample VCFs. Similar to the Pseudomonas example provided in the VCF_creator user guide (pages 4-5), we see a large number heterozygous genotypes despite all the samples being from haploid organisms (e.g. 0/0, 0/1, 1/1). How should we interpret these heterozygous reads from our bacterial sequence data (paired-end data provided in the fof_reads1.txt and
fof_reads2.txt structure as described in Case 4 of the discoSNP user guide). Any guidance appreciated!
Hi

The genotyping is an option that can be switched off (`-n` option) when working on non diploid species. Computing the genotype on haploid species is meaningless. 

However, 0/1 results may warn you (depending on the effective coverage of each allele) as this may reflect the existence of approximate repeats in the genome `-----A------//------T-------`  that may be seen as SNP variants while they are not. 

1/1 results are expected as, with no reference genome, the "reference" allele is randomly chosen and an homozygous variant may fall in the other allele. 

Hope this helps; 
Pierre

