How can one annotate a VCF file and transform it into a list of genes with specified mutations?

Question

[emilydolivo5]

I have fastq files generated using multiplex MinION nanopore sequencing (long reads) on a specific fungus, I employed minimap2, samtools, and freebayes to generate my VCF file. I have two questions:

Which tool should I use to trim reads before minimap2, considering that I need a tool that not only allows me to specify read length but also permits me to specify the read size to trim in the 5' prime?

How can I annotate a VCF file and transform it into a list of genes with specified mutations?

If you have a tutorial, steps, or scripts to address these questions, I would greatly appreciate your assistance. Thank you in advance, and I hope to receive answers to my inquiries!

[GenoMax]

I need a tool that not only allows me to specify read length but also permits me to specify the read size to trim in the 5' prime?

bbduk.sh with minlen=NN maxlen=NN forcetrimleft=NN options. Other trimming programs will likely have similar options (fastp etc).

A guide is available: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/

How can I annotate a VCF file and transform it into a list of genes with specified mutations?

snpEff, VEP and like. VEP Tutorial: http://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html