(SV) slim down REF column for CPX variants #4970
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@@ Coverage Diff @@
## master #4970 +/- ##
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+ Coverage 60.198% 80.791% +20.593%
- Complexity 12781 17962 +5181
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Files 1095 1095
Lines 64604 64594 -10
Branches 10394 10392 -2
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+ Hits 38890 52186 +13296
+ Misses 21482 8384 -13098
+ Partials 4232 4024 -208
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cwhelan
reviewed
Jul 5, 2018
| final Allele anchorBaseRefAlleleRear = Allele.create(refBases[refBases.length - 2], true); | ||
| final SimpleInterval startAndStop = makeOneBpInterval(complexVC.getContig(), complexVC.getEnd()); | ||
| final VariantContextBuilder rearIns = getInsFromOneEnd(false, firstRefSegmentIdx, startAndStop, anchorBaseRefAlleleRear, refSegmentLengths, altArrangement, true); | ||
| final int pos = complexVC.getEnd(); |
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Why is it the end of the VC here and not the start?
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The reason was because this is for extracting rear insertion.
Example:
SEGMENTS=chr1:100-200,chr1:200-300,chr1:300-400,chr1:400-500
ALT_ARRANGEMENT=chrOther:100-158,1,-3,4,UINS-433
Here we would emit four records:
a front insertion of 59 bases at position chr1:100, a deletion of chr1:200-300, an inversion of chr1:300-400, and a rear insertion of 433 bases at position of chr1:500.
cwhelan
approved these changes
Jul 5, 2018
* before all bases from affected region is extracted, leading to bloated VCF, now only the anchor base * also fixes downstream CPX variant re-interpreter
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Made a stupid decision to output all bases of the affected reference region, which significantly increased the VCF file size.
Now we follow the example for
DELvariants, i.e. we only put the reference base in POS in the REF column.