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COmbining gvcf files combing from TVC v.5.0.2
Dear GATK team,
I apologize if this is not the right place to ask, but I'm kind of desparate to find a solution to this...
so, I have installed the standalone version of TVC to get variants from Ion-Torrent bam files. TVC 5.0.2 can produce gVCFs. Thus, I was hoping that GATK will be able to combine them in a single VCF containing all samples and appropriate for population genetics analysis. Unfortunately, GATK crashes:
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: java.lang.Integer cannot be cast to java.lang.Double
I guess this is happening because the genome.VCF I have is produced with TVC and not GATK. Is that right?
Do you have a solution to this? Are there tools that could combine gvcf files produced by TVC?
thanks a lot in advance