It calculates total reads, depth of coverage, stdev, coefficient of variation, and both raw and demultiplexed, against a set of regions, takes minMQ, minFM, and maxDepth and padding parameters.
It requires a bed file currently, though I should modify the code to work with the intervals in the bam header.
bmftools depth is currently live.
It calculates total reads, depth of coverage, stdev, coefficient of variation, and both raw and demultiplexed, against a set of regions, takes minMQ, minFM, and maxDepth and padding parameters.
It requires a bed file currently, though I should modify the code to work with the intervals in the bam header.