Hello,
I am using NGS to obtain data from a couple of isolates of one species. The isolates seem to be very similar to each other, sharing a lot of genetic variation (SNPs).
I managed to phase the SNPs using HapCompass in each isolate and produce a VCF file with phased data in blocks.
How would I proceed if I want to use VCF tools to detect the rate of recombination (places where the phases of SNPs in some isolates might be different from other isolates)?
My organism is tetraploid, so the phases are 0|0|0|1, what tools could I use to measure LD or detect cross-over events?
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