After running svim-asm haploid, I found some of tandem duplications were filtered "not_fully_covered".
To understand their duplication pattern, I figured every alignments overlapping with those duplication; but the duplication pattern were not obvious. (I have attached a illustration of a "not_fullly_covered" duplication with corresponding alignments)
What exactly does it mean by "'not_fully_covered" besides the description in variant.vcf, "Tandem duplication is not fully covered by a contig"?
Moreover, is there any way to get SV coordinates from query, too?
Hello,
After running svim-asm haploid, I found some of tandem duplications were filtered "not_fully_covered". To understand their duplication pattern, I figured every alignments overlapping with those duplication; but the duplication pattern were not obvious. (I have attached a illustration of a "not_fullly_covered" duplication with corresponding alignments) What exactly does it mean by "'not_fully_covered" besides the description in variant.vcf, "Tandem duplication is not fully covered by a contig"? Moreover, is there any way to get SV coordinates from query, too?
duplication not fully covered.pptx
Kind regards Charyeong from Konkuk University, Seoul