I want to write translocations/duplications in VCF, however, I am unable to find out what is the correct syntax for that.
Let's say that there is a translocation (cut and paste event) from genome A (position Chr1:100-120) to genome B (position Chr2: 250-270), and a duplication in genome A compared to genome B so that in genome A the region is present twice (at Chr3:50-70 and Chr5: 90-110) while in genome B only once (at Chr5:90-110). Here, we can consider genome A as the reference. Now, is it possible to provide this information in VCF? If yes, then how would it look like? If not, then are there any alternate formats to store this information?
I read the documentation, but unfortunately, it was not clear enough for me and I still do not have answers to my questions. Any help would be highly appreciated.
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It's not trivial and I cannot claim I fully understand it myself. One page worth reading is this one: https://simpsonlab.github.io/2015/06/15/merging-sv-calls/