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Zev Kronenberg @zevkronenberg
Summarize covered vs. uncovered bases: samtools depth -aa your.sorted.bam | perl -lane 'if ($F[2] > 0){ $F[2] = 1} print join "\t", @F' | bedtools groupby -g 1 -c 3,3 -o distinct,count > info.txt #clFoo #perl #bedtools
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