No empty alts if you please [VS-918] #8326
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8326 +/- ##
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Coverage ? 86.193%
Complexity ? 35521
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Files ? 2192
Lines ? 166470
Branches ? 17918
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Hits ? 143485
Misses ? 16601
Partials ? 6384 |
rsasch
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May 17, 2023
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| ### Run GvsCreateVATfromVDS | ||
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| Note: in order for this workflow to run successfully the 'Use reference disks' option must be selected in Terra workflow |
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| Note: in order for this workflow to run successfully the 'Use reference disks' option must be selected in Terra workflow | |
| **Note:** in order for this workflow to run successfully the 'Use reference disks' option must be selected in Terra workflow |
RoriCremer
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May 17, 2023
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The empty alts that results from overtrimming in an alt allele UDF correlate strongly with VAT / alt allele mismatches, but from trial runs with and without this patch they don't seem to actually be causing the mismatches. Nonetheless I think this is a desirable change as it keeps VAT VIDs from getting weird. VIDs have the format
<contig>-<position>-<ref>-<alt>; if the alt is empty the VID just ends in a dash which just seems like an edge case waiting to break something.