I used the following pipeline to call SNPs on an alignment file:
$ samtools mpileup -uf s_cerevisiae.fasta aln.sorted.bam | bcftools view -O b - > snps.bcf $ bcftools view snps.bcf | vcfutils.pl varFilter -D 100 -Q 20 > snps.vcf
The purpose of the second step is filtering calls with more than 100 read depth and those with less than 20 mapping quality. When I look at the output VCF file, however, it seems that all the calls have 0 in the QUAL column. This is true for all the samples I called SNPs for. So I am a little bit confused– would appreciate any clarification.