It appears like nf-core sarek can only be used to call variants using short reads and not PacBio HiFi because the

samplesheet

and mappers are all meant to be used in short reads variant calling?

Hi, @Javan Okendo! Slack uses channels to organise discussions. Press the

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more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @mashehu for help.

For sarek questions, you can ask in #CGFUX04HZ, but also have a look at #C07MFUQAR1B and maybe #C09FN9T5GQH. (I have not tried those, and they are not as mature as sarek, but they might work for your use case.)