https://bioinformaticsonline.com/snippets/view/36254/genome-covered? https://bioinformaticsonline.com/snippets/view/36254/genome-covered Tue, 17 Apr 2018 14:13:05 -0500 https://bioinformaticsonline.com/snippets/view/36254/genome-covered zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1) nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc <<< "scale=6; ($nonzero / ($zero + $nonzero))*100") echo $percent]]> Neel