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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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( AC / NUM_MERGED_SVS ) < 25 #149

Open weizhu365 opened 8 months ago

weizhu365 commented 8 months ago

"( AC / NUM_MERGED_SVS ) < 25" is part of the published paper of GraphTyper2. I cannot figure out what its purpose is. Could you explain it to me?

Thanks,

Wei

Wei Zhu

hannespetur commented 6 months ago

Hey,

NUM_MERGED_SVS is (roughly) the amount of samples where the SV was discovered in. AC is the number of haplotypes graphtyper calls the SV. So the point of the filter is to removes SV that are discovered in a lot fewer samples than it is called in. Usually when it happens it is because the rare SV breakpoint sequence is very similar to another common variant (i.e. a small indel)

Best, Hannes