How to implement sarek for plant variant calling？

[meng-hhh]

Description of feature

Can sarek be used for variant calling in plant genome? And if possible, what should be done?

[FriederikeHanssen]

I am afraid I have no direct experience with plant genomes. In principle, you should be able to use sarek but you likely need to set up your reference genomes. For this we have some guidance here: https://nf-co.re/sarek/3.4.4/docs/usage/#no-igenomes-reference-files-are-used

You will need the fasta file as a minimum requirement. Some of the tools run along the way require other databases as input: base recalibration, for example, requires a DBSNP file, or the annotation tools require the respective caches.

Which plant genome are you interested in and which tools would you like to run?