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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR convertAssemblytics problem #128

Closed MehmetGoktay closed 4 years ago

MehmetGoktay commented 4 years ago

Hi Fritz,

I am interested in a tandem duplication event on one of the chromosome. We already know that one of the sample contains 4 extra copies. When I use assemblytics to call it. It identifies as tandem_expansion with 4 extra copies.

3 12363708 12379593 Assemblytics_b_1315 15883 + Tandem_expansion -15885 -2 ourAssembly_Contig_20:15168814-15168816:- between_alignments 3 12363708 12379593 Assemblytics_b_1315 15883 + Tandem_expansion -15885 -2 ourAssembly_Contig_20:15168814-15168816:- between_alignments 3 12363708 12379593 Assemblytics_b_1317 15883 + Tandem_expansion -15885 -2 ourAssembly_Contig_20:15168814-15168816:- between_alignments 3 12363708 12379593 Assemblytics_b_1318 15883 + Tandem_expansion -15885 -2 ourAssembly_Contig_20:15168814-15168816:- between_alignments

So far so good. Length is correct with 15885.

But when I use SURVIVOR convertAssemblytics to creates this insertions with size 31768.

3 12363708 Assemblytics_b_1315 N . LowQual IMPRECISE;SVTYPE=INS;SVMETHOD=Assemblytics;CHR2=1;END=12379593;SVLEN=31768;PE=1 GT 1/1 3 12363708 Assemblytics_b_1316 N . LowQual IMPRECISE;SVTYPE=INS;SVMETHOD=Assemblytics;CHR2=1;END=12379593;SVLEN=31768;PE=1 GT 1/1 3 12363708 Assemblytics_b_1317 N . LowQual IMPRECISE;SVTYPE=INS;SVMETHOD=Assemblytics;CHR2=1;END=12379593;SVLEN=31768;PE=1 GT 1/1 3 12363708 Assemblytics_b_1318 N . LowQual IMPRECISE;SVTYPE=INS;SVMETHOD=Assemblytics;CHR2=1;END=12379593;SVLEN=31768;PE=1 GT 1/1

So it basically creates 4 Insertions with a doubled size. I would be fine if it was showing 4 insertions with the length of 15883 instead of 31768 (doubled). Or as a duplication event.

Could you please kindly tell me if there is a way to do this or is this just the way that survivor works.

Best, Mehmet

fritzsedlazeck commented 4 years ago

Dear Mehmet, thanks for pointing this out. I indeed found (I think) the cause of this problem. I have pushed the correction to github. Would you mind testing it out and see if that solves it?

Thanks Fritz

MehmetGoktay commented 4 years ago

Hi Fritz,

I have tested it and it works now.

Thanks, Mehmet

fritzsedlazeck commented 4 years ago

thanks for letting me know. Fritz