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#112 fix wrong alleles in variant reports

0.2
closed
Wolfgang Maier
bug-fix (41)
2020-12-02
2019-03-14
Wolfgang Maier
No

study and fix a bug in remap that causes (occasional?) non-rv-complementing of nucleotides on the reverse strand?

It turns out this isn't a bug in the remap tool, but in the varreport tool.
It parses alleles from the SnpEff-annotated effects, but this lists REF/ALT alleles with respect to the affected feature. So the tool reports rv-complemented alleles for features on the rv strand :(

Discussion

  • Wolfgang Maier

    Wolfgang Maier - 2020-10-08
    • summary: fix remap rv strand bug --> fix wrong alleles in variant reports
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -1 +1,5 @@
 study and fix a bug in remap that causes (occasional?) non-rv-complementing of nucleotides on the reverse strand?
+
+-----
+It turns out this isn't a bug in the remap tool, but in the varreport tool.
+It parses alleles from the SnpEff-annotated effects, but this lists REF/ALT alleles with respect to the affected feature. So the tool reports rv-complemented alleles for features on the rv strand :(
     

  • Wolfgang Maier

    Wolfgang Maier - 2020-10-09

    correction to the correction: the real cause of the issue is that the SnpEff effect allele (which SnpEff writes correctly in every case) can get out of sync with the ALT column during rebasing (which may rv-complement ALT alleles, but doesn't know about SnpEff effects fields).

     

  • Wolfgang Maier

    Wolfgang Maier - 2020-12-02
    • status: open --> closed
     

  • Wolfgang Maier

    Wolfgang Maier - 2020-12-02

    fixed by [2482ec]

     

    Related

    Commit: [2482ec]

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