Further processing after alignment using Winnowmap

marbl / Winnowmap

Long read / genome alignment software

Other

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Further processing after alignment using Winnowmap #21

Closed dKlee99 closed 3 years ago

dKlee99 commented 3 years ago

Which workflow / tools do you recommend to follow after aligning and filtering using Winnowmap? Should I follow standard minimap2 workflow after aligning? Thanks for your amazing works!

dKlee99 commented 3 years ago

especially for variant calling, do you recommend using widely-used GATK Haplotype Caller? or sniffles for SV calling?