/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools mpileup -uf /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome.fa -F 1 -b samtools-mpileup.files | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/bcftools/bcftools view -bvcg - > STAR-alignments.raw.bcf