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I've done with a run of HaplotypeCaller on my samples. I'm now analysing everything with snpEff, although I'm doing this "outside" GATK. I had to stop the analysis because a huge number of errors, all dealing with indels, such as:
Error while processing VCF entry (line 580649) : chr21 26718345 . TAATCCTGAGTTTAA TATCCTAAATGTTTAC 943.26 […] java.lang.RuntimeException: Insertion '-A+AT' does not start with '+'. This should never happen! chr21 35260360 . CATAACAGTTCAT AGAGACAGAG 425.22 […] java.lang.RuntimeException: Deletion '+G-TTC' does not start with '-'. This should never happen!
Of course, this is a snpEff error, nevertheless the Indel format looks quite different from what I've ever seen. Consider the first line above: shouldn't it be like
chr21 26718345 . AT T 943.26 […]
(I can't resolve the second right now).
Any hint is appreciated at this point. I'm writing to snpEff developer for the same reason...