https://bioinformaticsonline.com/snippets/view/36256/coverage-depth-of-reads? https://bioinformaticsonline.com/snippets/view/36256/coverage-depth-of-reads Tue, 17 Apr 2018 14:18:44 -0500 https://bioinformaticsonline.com/snippets/view/36256/coverage-depth-of-reads # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get length of reference genome bowtie2-inspect -s refgenome | awk '{ FS = "\t" } ; BEGIN{L=0}; {L=L+$3}; END{print L}' 45678]]> Neel