Mean coverage from a BAM one-liner

Calculates the mean depth of mapped coverage over the whole genome from a mapped bam, using bedtools

bedtools genomecov -ibam  -g bedtools_genome.txt \
 | awk '$1=="genome" {tot += $2*$3; reads += $3} END {print tot/reads}'

To generate bedtools_genome.txt use

samtools faidx reference.fa
cut -f 1-2 reference.fa.fai > bedtools_genome.txt
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