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SUwonglab / arcsv

Complex structural variant detection from WGS data
MIT License
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Can arcsv genotype samples using a ref complex-SV vcf files #2

Closed songtaogui closed 6 years ago

songtaogui commented 6 years ago

Hi,

Thank you for developing this wonderful tool.

I have learned that arcsv can call complex-SVs in each sample. I was wondering that is it possible that I merge all sample's complex-SV calls into one file, and use the merged SVs to genotype all the samples? Or if I identified some complex-SVs by comparing two genomes, could I use arcsv to genotype these SVs in population samples?

Thank you

Best wishes, Songtao Gui

jgarthur commented 6 years ago

Thanks for the feedback! To answer your questions:

1) I have observed many SVs called identically in multiple samples, so a simple de-duplication step may be sufficient here. Merging different SVs into a common one is a tricky problem, however -- even for simple SVs. 2) Genotyping new samples based on an existing set of complex SVs (from ARC-SV or somewhere else) is not possible, unfortunately. ARC-SV is actually very well-suited to this task, so some genotyping-only mode may be added in the future.

songtaogui commented 6 years ago

Dear Joey,

Thank you for you reply.

I will try merging each sample's SV .

Best wishes,

Songtao Gui