Usually when I do SNP calling, I do this:
samtools mpileup -g -f Ref.fa File.bam | bcftools view -cv -
where samtools outputs a bcf file and bcftools does the SNP calling.
I can also get a pileup file by running (no bcf output):
samtools mpileup -f Ref.fa File.bam
which is basically a list of nucleotide positions and their bases and errors.
Now I'm playing around with SNP calling and I'd like to call bcftools on a modified pileup file.
Is it possible to call bcftools with a pileup file and not a bcf file? Or do I need to use another SNP caller?