a7cb599945
-Throw a UserException if a Locus or ActiveRegion walker is run with -dcov < 200, since low dcov values can result in problematic downsampling artifacts for locus-based traversals. -Read-based traversals continue to have no minimum for -dcov, since dcov for read traversals controls the number of reads per alignment start position, and even a dcov value of 1 might be safe/desirable in some circumstances. -Also reorganize the global downsampling defaults so that they are specified as annotations to the Walker, LocusWalker, and ActiveRegionWalker classes rather than as constants in the DownsamplingMethod class. -The default downsampling settings have not been changed: they are still -dcov 1000 for Locus and ActiveRegion walkers, and -dt NONE for all other walkers. |
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| .. | ||
| annotator | ||
| beagle | ||
| bqsr | ||
| compression/reducereads | ||
| diagnostics | ||
| diffengine | ||
| fasta | ||
| filters | ||
| genotyper | ||
| haplotypecaller | ||
| indels | ||
| phasing | ||
| validation | ||
| varianteval | ||
| variantrecalibration | ||
| variantutils | ||