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DecodeGenetics / graphtyper

Population-scale genotyping using pangenome graphs
http://dx.doi.org/10.1038/ng.3964
MIT License
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Filtering SVs after genotyping by Graphtyper2 #70

Closed Saeideh-Ashouri closed 3 years ago

Saeideh-Ashouri commented 3 years ago

Hi. I have run Manta on short-read data of 100 sample, got the union of SV sites using svimmer, and used Graphtyper2 to genotype the SVs. For some SVs there were more than one record in final VCF file. So, I used exactly the same filters mentioned in the supplementary information of your paper in NC, however, after filtering the data, there are still SVs with more than one record in the final VCF file. What do you recommend me do? Do I need to change the criteria for filtering the variants? Any inputs will be highly appreciated.

Thank you in advance,

hannespetur commented 3 years ago

Hi, use only the aggregated model (INFO/SVMODEL=='AGGREGATED'), there should only be one such record for each SV. This perhaps should have been made clearer in the supplementary.

Best, Hannes

Saeideh-Ashouri commented 3 years ago

Thank you so much for your prompt reply. I added SVMODEL = AGGREGATED to the filtering command in the supplementary file (the one for filtering SV sites using vcffilter) and it worked.

Thanks again, Best, Saeideh