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How to interpret when Tandem duplications are filtered "not_fully_covered"? #24

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cherryCookies opened this issue Jul 12, 2023 · 0 comments

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@cherryCookies
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cherryCookies commented Jul 12, 2023

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

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