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I am looking at the Manta structural variant caller https://github.com/Illumina/manta. I successfully got it to work however, I am unsure of how to process the outputs further. I am particularly interested in the `diploidSV.vcf.gz` file but when I try to process it through ANNOVAR it doesn't work. What should I do to process this output further?
I think I am already stressed out by it but I have processed a lot data with Manta and I kind of need the results so you as saying Illumina's Manta can be fed into Illumina's Nirvana (https://github.com/Illumina/Nirvana)? Have you used it with Manta before?
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