Depth-Weighted Interval Sharding
A standalone Terra/Cromwell WDL pipeline that splits variant-calling intervals
into work-balanced shards instead of equal-size genomic shards.
GATK SplitIntervals balances shards by base count. But Mutect2’s runtime and
memory scale with the number of reads it processes, which is roughly
mean_depth × bases. On a mixed WES + targeted-panel design, the panel regions
are sequenced far deeper than the exome, so equal-size shards land very uneven
amounts
This is a companion discussion topic for the original entry at github.com/gulhanlab/depth_weighted_sharding/DepthWeightedSharding