FreeBayes detection capacity

Question

[quentinperriere]

Hello,

I'm currently utilizing FreeBayes for variant detection with reads generated through Oxford Nanopore technology. However, I've encountered an issue where not all known variants (SNPs and insertions) that I expect to detect are being generated. Below is the command and parameters I'm using:

freebayes -f path/ref_sequence -L path/bam_file --vcf path/output_vcf_file --ploidy 2 --min-alternate-fraction 0.05

It's worth noting that my BAM files were generated using Minimap2. I'm curious if there's a method to enhance FreeBayes' capability for variant detection. Any insights would be greatly appreciated. NB1 : I'm working on fungus NB2 : it's important for me to work with freebayes , that's why I'm looking for a solution