I have generated a vcf file using bcftools pileup and bctools call using this code:
bcftools mpileup -Ou -f ref.fa in.bam | \
bcftools call -mv -Ov -P 0.5 -o out.vcf
Comparing the bam file and the vcf file with IGV I see in some places that in the bam file there are di or trinucleotide variants while in the vcf file I see only snv. Any ideas on how to fix it/or why the vcf ouput is correct?