45fc0ea98d
-- Now calculates the number of Indels overlapping gold standard sites, as well as the percent of indels overlapping gold standard sites
-- Removed insertion : deletion ratio for 1 bp event, replaced it with 1 + 2 : 3 bp ratio for insertions and deletions separately. This is based on an old email from Mark Daly:
// - Since 1 & 2 bp insertions and 1 & 2 bp deletions are equally likely to cause a
// downstream frameshift, if we make the simplifying assumptions that 3 bp ins
// and 3bp del (adding/subtracting 1 AA in general) are roughly comparably
// selected against, we should see a consistent 1+2 : 3 bp ratio for insertions
// as for deletions, and certainly would expect consistency between in/dels that
// multiple methods find and in/dels that are unique to one method (since deletions
// are more common and the artifacts differ, it is probably worth looking at the totals,
// overlaps and ratios for insertions and deletions separately in the methods
// comparison and in this case don't even need to make the simplifying in = del functional assumption
-- Added a new VEW argument to bind a gold standard track
-- Added two new stratifications: OneBPIndel and TandemRepeat which do exactly what you imagine they do
-- Deleted random unused functions in IndelUtils
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|---|---|---|
| .. | ||
| CNV | ||
| activeregionqc | ||
| annotator | ||
| beagle | ||
| bqsr | ||
| coverage | ||
| diagnostics | ||
| diffengine | ||
| fasta | ||
| filters | ||
| genotyper | ||
| indels | ||
| phasing | ||
| qc | ||
| recalibration | ||
| validation | ||
| varianteval | ||
| variantrecalibration | ||
| variantutils | ||
| BAQIntegrationTest.java | ||
| ClipReadsWalkersIntegrationTest.java | ||
| PileupWalkerIntegrationTest.java | ||
| PrintReadsIntegrationTest.java | ||
| PrintReadsUnitTest.java | ||