Neel
Bioinformatics Beginner
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By Neel 2411 days ago
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
