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The ComputeReadDepthCoverage walker traverses a set of BAM files to generate genome-wide read depth statistics.
The read depth coverage is the number of fragments confidently aligning to the genome (or interval if an interval subset is used). The read depth coverage is measured only at confidently alignable bases (based on the genome mask) and only using reads passing the mapping quality filter. Reads are counted as aligning at the middle aligned base. Sequenced molecules are counted only once: for paired-end data, only the leftmost end of the pair (the end with the lowest reference coordinate) is counted.
Read depth coverage is computed and reported for each readgroup, but the output is keyed by sample and library to allow easy roll up.
See also MergeReadDepthCoverage.
-I <bam-file> : The set of input BAM files.
-minMapQ <quality-threshold> : Reads below this mapping quality are not
-excludedReadGroups <file> : Optional file containing a list of read
groups to ignore (one read group per line).
-genomeMaskFile <mask-file> : Mask file that describes the alignability of
the reference sequence. : See Genome Mask Files.
-O <coverage-file>: Tab delimited output file (default is stdout).
Geraldine Van der Auwera, PhD