Updating splice site logic. #5106
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Now ignores leading indel bases when checking if variants are within the
splice site boundaries (i.e. if a leading base in an indel, which is
preserved between the reference and alternate alleles, is within the
splice site boundary but the bases that have been changed are NOT,
then the variant is now correctly labeled as NOT a splice site).
Fixes #5050
droazen
reviewed
Aug 14, 2018
| @@ -1320,9 +1347,16 @@ private static GencodeGtfExonFeature getExonWithinSpliceSiteWindow( final Varian | |||
| final int spliceSiteVariantWindowBases ) { | |||
| GencodeGtfExonFeature spliceSiteExon = null; | |||
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| final int varStart = FuncotatorUtils.getIndelAdjustedAlleleChangeStartPosition(variant); | |||
| final int varEnd = variant.getEnd(); | |||
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Why don't you repeat the logic above to set the end here?
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You're absolutely right - I need to update it.
I missed it because I was not using intervals to do the boundary checks.
Codecov Report
@@ Coverage Diff @@
## master #5106 +/- ##
=============================================
- Coverage 86.49% 86.49% -<.001%
- Complexity 29203 29262 +59
=============================================
Files 1814 1814
Lines 135364 135628 +264
Branches 15042 15068 +26
=============================================
+ Hits 117077 117305 +228
- Misses 12826 12854 +28
- Partials 5461 5469 +8
|
droazen
reviewed
Aug 14, 2018
| if ((Math.abs(exon.getStart() - variant.getStart()) <= spliceSiteVariantWindowBases) || | ||
| (Math.abs(exon.getEnd() - variant.getStart()) <= spliceSiteVariantWindowBases)) { | ||
| // Check the start and end of the variant to see if it overlaps with either end of the exon: | ||
| if ((Math.abs(exon.getStart() - varStart) <= spliceSiteVariantWindowBases) || |
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Can you use something like SimpleInterval.overlapsWithMargin() here?
Added more test cases and adjusted algorithm to account for inserted bases when dealing with insertions.
LeeTL1220
reviewed
Aug 15, 2018
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@jonn-smith One comment that might be no work. Feel free to merge once addressed.
| // NOTE: because there could be degenerate VCF files that have more than one leading base overlapping, we need | ||
| // to detect how many leading bases there are that overlap, rather than assuming there is only one. | ||
| final int varStart; | ||
| if ( GATKProtectedVariantContextUtils.typeOfVariant(variant.getReference(), altAllele).equals(VariantContext.Type.INDEL) ) { |
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I think you should also check that it is not a complex indel (GATKProtectedVariantContextUtils.isComplexIndel(...)), unless that is addressed upstream...
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Yup. Sounds good. Fixed!
jonn-smith
deleted the
jts_funcotator_splice_site_indel_boundary_fix_5050
branch
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Now ignores leading indel bases when checking if variants are within the
splice site boundaries (i.e. if a leading base in an indel, which is
preserved between the reference and alternate alleles, is within the
splice site boundary but the bases that have been changed are NOT,
then the variant is now correctly labeled as NOT a splice site).
Fixes #5050