I have created a vcf file from bam file using bcftools:
bcftools mpileup \ --redo-BAQ \ --min-BQ 30 \ --per-sample-mF \ --annotate \ FORMAT/AD,FORMAT/DP,INFO/AD -f cmv3 scaffold_nofilt_PV002.bam | \ bcftools call --multiallelic-caller --variants-only -Ov > \ PV002_nofilt.vcf
After that I visualized this file using R, but It had lower number of records in comparation to IGV program results using the same bam file. I think that it is due to bcftools take only SNP with high frequency.
What modification should do add to the bcftools program to see all records although they have a low frequency?