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haplotypecaller indel format

dcittarodcittaro Posts: 31Member
edited September 2012 in Ask the GATK team

Hi there, 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...

Post edited by Geraldine_VdAuwera on

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