Neel
Bioinformatics Beginner
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Coverage / Depth of reads !
By Neel 2411 days ago
# 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
