I used discoSNP to compare a set of NGS reads from three different samples (2 parental diploid species + the hybrid (allopolyploid) originated from them). In addition, I would like, as a control, to analyse SNPs in a virtual hybrid generated by mixing equal number of reads from each parental set and subjecting this data sets to the whole genome SNP analysis. Thus, all SNPs should be mapped back to the parental data sets while none of the SNPs should be "unique" for the electronic hybrid. right? But the problem is that I am not succeeding on doing this. Although I get the coherent.fa file, somehow discoSNP is getting stuck on the vcf file generation. It gives the following message:
/media/marques/DATA/SeqClust/Stylosanthes/DiscoSnp/scripts/run_VCF_creator.sh -p test-sampled-mix_k_31_c_auto_D_1_P_1_b_0_coherent.fa -o test-sampled-mix_k_31_c_auto_D_1_P_1_b_0_coherent.vcf ##use disco SNPS : test-sampled-mix_k_31_c_auto_D_1_P_1_b_0_coherent.fa ##output : test-sampled-mix_k_31_c_auto_D_1_P_1_b_0_coherent.vcf !!! Disco file can't be a sam file !!! there was a problem with VCF creation. See how to use the "run_VCF_creator.sh" alone.
Could you help me with this issue?