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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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Duplications in previous version #151

Closed annerilotter closed 2 years ago

annerilotter commented 2 years ago

Hi

I have run the previous version of SyRi between two haplogenomes and the duplication total sizes in the reference seem to be double of that in the query.

Is there an issue in v4 that would cause this:

Structural annotations

Variation_type Count Length_ref Length_qry

Syntenic regions 15245 256751376 256583791 Inversions 187 55557398 54570060 Translocations 10502 86591743 86799621 Duplications (reference) 19302 145450405 - Duplications (query) 18916 - 63010166 Not aligned (reference) 22849 62437935 - Not aligned (query) 24754 - 72125631

Sequence annotations

Variation_type Count Length_ref Length_qry

SNPs 8350925 8350925 8350925 Insertions 694782 - 8043419 Deletions 681344 7603918 - Copygains 2128 - 9884667 Copylosses 2135 9326217 - Highly diverged 7931 39641637 37649655 Tandem repeats 269 680104 653045

The reciprocal alignment gave this:

Structural annotations

Variation_type Count Length_ref Length_qry

Syntenic regions 15236 256747807 256876296 Inversions 189 54233806 55605620 Translocations 10526 89269151 88801518 Duplications (reference) 21149 159115873 - Duplications (query) 16865 - 55495066 Not aligned (reference) 24700 72234120 - Not aligned (query) 22770 - 62322133

Sequence annotations

Variation_type Count Length_ref Length_qry

SNPs 8376569 8376569 8376569 Insertions 676636 - 7629721 Deletions 704383 8412691 - Copygains 2172 - 9578692 Copylosses 2127 9689158 - Highly diverged 8018 38129322 40181747 Tandem repeats 268 656872 680693

mnshgl0110 commented 2 years ago

I cannot recall anything in v1.4 that could result in this. Have you tried with the newer version?