#bcftools mpileup -o LVS_pile.bcf -f NC_007880_short.fasta LVS-sorted.bam

for f in *.bam

do
  PREFIX="${f%-sorted.bam}"
  bcftools mpileup -o $PREFIX\_pile.bcf -f NC_007880_short.fasta $PREFIX\-sorted.bam
  bcftools call -cv $PREFIX\_pile.bcf > $PREFIX\_variant.bcf

shift
done