Hi all,
By a genotyping by sequencing approach I have sequenced12 wild type and 12 mutants of Arundo donax, and did de novo assembling (software STACKS) of the reads.
I have several files in the vcf and .tsv formats with haplotype polymorphisms, SNPs. My idea was to detect and use the deletion polymorphisms generated by the irradiation, in order to characterize each mutant. With deletion polymorphism I mean for example the haplotypes lost due to the effect of the mutagenesis.
Can anyone suggests if there is some statistics modellization (i.e. in my vcf file I have information about genotype type and the total depth for each of haplotype polymorphism) I can apply to do this kind of analysis or possibly suggests some reference useful for my purpose?
Unfortunately for Arundo donax there is only the transcriptome reference available and no other genetic/genomic information.
I really appreciate any help!
