Genome-wide polymorphism analysis: after using freebayes to identify SNP and Indel, I will follow these criteria for filtering: (1) the minimum variant frequency of ≥ 90%, (2)average quality of the SNP base ≥ 30 and minimum read depth of 10.
Question1: what kind the tools can be used for these criteria filtering?
Question2: After variation filtering, I'm curious about how to compare the SNPs/Indel difference between cultivars? I analyzed re-sequencing data between four cultivars.
For example, there are A, B, C and D cultivars in the vcf file. But I would like to compare the SNP/Indel variance between A/B and A/C (such as SNP/Indel number)
Thank you very much