How can I detect small deletion
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7 months ago
dyfn1947 • 0

Hello! thanks for reading this question. I did reference mapping use WGS data (minimap2), and snp, indel calling using GATK. But they didn't detect small deletion(500bp) , I'm sure they have small deletion(500bp) because my coworker already checked deletion using conventional mapping. How can I detect and prove the small deletion? Thanks.

SNP indel GATAk • 195 views
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Hi, you can use Manta https://github.com/Illumina/manta

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