I recently apply my attentions on analysis of structure variants (SV) with called vcf file. I have read the The VCF specification V 4.2 from https://github.com/samtools/hts-specs. I noted the SVTYPE called BND is useful for my work. But I have some confused question on its ALT field.
Fistly, the specification descirbed the field as follow:
This is easily to understand about the breakpoint positions and its mate breakpoint. But I am not sure how to find the correct direction of the fragment? for clearly my question, please allow me show another exmaple, the following picture shows a INV in chr2: 321682 - 421682.
I can understand the 321681 is linked 421681 like the upward picture shows.
But why we cant let 321682 link to 421682 like following, is only because position 321681 has been discovered?
One more question, are there any package has been developed to help us process the ALT feild of SVTYPE is BND?
Thanks for your reading.