How can I detect small deletion

Question

[dyfn1947]

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.

[German.M.Demidov]

Hi, you can use Manta https://github.com/Illumina/manta