i have a bam file (also a bed file getting from bam to bed in galaxy), and a fasta.fai reference genome
i need genome coverage, i tried many ways, at last i found a post telling this command
samtools mpileup -ABQ0 -d10000000 -f ref.fas qry.bam > qry.mpileup
im in window
my refence genome name is= sequence.fasta.fai
my bam file name is= eg1.bam
and both files placed in
now, which i should type in cmd instead of above command???