BAM/CRAM depth calculation biological sequencing


Many small reads are produced by high-throughput "next generation" sequencing technologies. The final sequence is derived from how these reads are overlapping towards a consensus. The more reads are covering/confirming parts of a nucleotide seq, the higher the confidence is. Too many reads would be indicative of e.g. repeats in the genome.

mosdepth can output:
 * per-base depth about 2x as fast samtools depth--about 25 minutes
    of CPU time for a 30X genome.
 * mean per-window depth given a window size--as would be used for
    CNV calling.
 * the mean per-region given a BED file of regions.
 * a distribution of proportion of bases covered at or above a given
    threshold for each chromosome and genome-wide.
 * quantized output that merges adjacent bases as long as they fall
    in the same coverage bins e.g. (10-20)
 * threshold output to indicate how many bases in each region are
    covered at the given thresholds.
when appropriate, the output files are bgzipped and indexed for ease of use.

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