No alt reads for called SNPs

[grasshoffm]

I am calling SNPs with bcftools mpileup and bcftools call.

I use the output vcf as an input for vartrix. In the vartrix result, there are positions that have no alt reads for any cell.

Shouldn't there be at least one cell per position, that has alt reads?

Here is the code, that I used.

bcftools mpileup -Q 30 -A -x -O u -f $REFERENCE_FASTA $BAM | bcftools call -mv > $OUT_DIR/${SAMPLE}.vcf

vartrix_linux --threads $ncores --mapq 30 --bam $BAM --vcf $OUT_DIR/${SAMPLE}.vcf --scoring-method "alt_frac" --cell-barcodes $CELLS --fasta $REFERENCE_FASTA --out-matrix ${out_matrix}