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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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sv.vcf output DEL and DUP annotations for almost identical genomics regions #113

Open huanwang1985 opened 7 years ago

huanwang1985 commented 7 years ago

Hi,

I'm trying to get CNV annotations for a single paired end WGS sample, and the implementation works fine. No error is produced. But when I was looking into the result sv.vcf file , it looks like some regions are annotated as both DEL and DUP. This doesn't make much sense to me. Could you please help me out and briefly explain what possible causes might be?

Examples shown as below

[huanwang@Huan-Wangs-MacBook-Pro VCFs 12:30 PM]$  grep -E '29204439|29204459' BB_ID012737_noRealign.sv.vcf
16  29204439    1390    N   <DUP>   .   .   SVTYPE=DUP;STRANDS=-+:10;SVLEN=58988381;END=88192820;CIPOS=-249,10;CIEND=-10,763;CIPOS95=-99,2;CIEND95=-2,230;IMPRECISE;SU=10;PE=10;SR=0    GT:SU:PE:SR ./.:10:10:0
16  29204459    1391    N   <DEL>   .   .   SVTYPE=DEL;STRANDS=+-:4;SVLEN=-58988183;END=88192642;CIPOS=-10,837;CIEND=-600,10;CIPOS95=-3,165;CIEND95=-273,2;IMPRECISE;SU=4;PE=4;SR=0 GT:SU:PE:SR ./.:4:4:0

Thanks a lot!

Huan Wang