VCF output file format (ALT allele frequency)

[zdk427]

Hi there,

I am trying to detect SNVs from reads obtained after Oxford nanopore run.
After basecalling, minimap2 alignment, I am trying to run the resulting bam files for variant calling through:

ngs@ngs-ThinkCentre-M93p:/Desktop/longshot$ export PATH=$PATH:/home/$USER/.cargo/bin
ngs@ngs-ThinkCentre-M93p:/Desktop/longshot$ longshot -P 0.01 --bam trial2/A1.bam --ref trial2/JEV-Nakayama-NCBIreference.fasta --out A1.vcf

i have few variants but i am unable to interpret the ALT allele frequency for the respective variants.

is there any specified flag or option i need to mention for getting the allele frequency in the VCF file??

Thanks