Closed Milia1368 closed 5 months ago
Thanks for bringing this to my attention! There was a bug with incorrect size assignment when no sequences are included (the "4" and "0" are the difference between the non-sequence ALT seq "\<DEL>" or "
For the genotypes, SVrefine only reports as many alleles as there are query entries aligned to the reference. In the case of single-allele genotypes (e.g., "1"), only one contig from your assembly aligned to that specific location. Hope that helps!
Also, if you can give the most recently-committed version of SVrefine a try and see if you get correct SV lengths for this example, that would be a great help. Thank you!
Thanks for your help! I tried it again and the SVLEN problem is solved. Here is the output:
My confusion has been solved, thanks a lot!
Hello, I use this tool to call SV from assembly-hap and the commands are listed as below: `
All was well done, but there are some formatting issues in the formed vcf file which I can't figure out : why are all SVLEN=4 or 0,and GT =1 or 0/1 , what does this meaning? Under what circumstances would this be the case? Could you give me some advice about this, so I can make it for subsequent evaluation?
Thanks!