I'm recently doing annotation on many single-sample SV vcf files from manta, but single-sample manta vcf freqently create bugs so I tried to convert manta vcf to bed format files.
Everything goes well but suddenly I'm confused by how to describe an insertion variant.
For example, a bed file:
# chrom Start End Variant_type Biologist_annotation Biologist_ranking 4 71552 9371067 DEL 4p- syndrom Pathogenic 5 723194 777000 DUP Benign 7 110276505 110478039 INS NA 11 66287088 66288847 DEL BBS1 internal frameshift Pathogenic 15 34735949 34806953 DEL Benign 16 1565629 1571297 DUP IFT140 tandem duplication Pathogenic
This example was from AnnotSV.
And for example:
Both two forms has the same start point but different end point. And from my view, the first form (the black) should be correct since the insertion can't change the position of the reference genome.
But appraently the AnnotSV do not think like I do, and I'm really not sure which form of bed file should I produce.
And for the example I drew, should it be:
# chrom Start End Variant_type Biologist_annotation Biologist_ranking 1 1234 **1235** INS NA NA
# chrom Start End Variant_type Biologist_annotation Biologist_ranking 1 1234 **1237** INS NA NA
Thanks for your time reading this.