Scorer extracts wrong genomic sequence

Scorer extracts a sequence that does not agree with the reference given in the VCF file. Error is:

[ERROR] Variant annotation error at 271631 2L_271631! Expected reference TTTT found gggt
java.lang.RuntimeException: Variant annotation error at 271631 2L_271631! Expected reference TTTT found gggt
at barna.astalavista.Scorer.scoreVariants(Scorer.java:504)
at barna.astalavista.Scorer.scoreSites(Scorer.java:1044)
at barna.astalavista.Scorer.callLoop(Scorer.java:145)
at barna.astalavista.AStalavista.call(AStalavista.java:131)
at barna.astalavista.Scorer.call(Scorer.java:134)
at barna.astalavista.Scorer.call(Scorer.java:31)
at barna.commons.launcher.Flux.main(Flux.java:198)