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@Shelia @Geraldine_VdAuwera I will submit a bug report for future convenience. I eventually was able to get GATK to accept the VCF by sorting the positions using python rather than Picard and using a nightly build of GATK.jar which allows the non-h…
@Geraldine_VdAuwera I sorted the VCF using Picard's SortVcf, both using a reference dictionary for mafa5 (same reference called in the VQSR command and generated by picard) and sorting based on the sequence contigs in the header. In both cases the s…
@pdexheimer @Shelia I appended sequence contigs to the header and added a correctly formatted info line as well. I then sorted to reads using: java -jar ~/picard.jar which sorts according to the sequence header. My new vcf looks like this: filefo…
Thanks for the responce Sheila. I appended sequence contigs to the vcf and sorted it in order. I am still thrown the same error. I also cannot get VariantsToVCF to work on Bed files downloaded from dbsnp. Can you give me an example bed file that wil…
Sorry, I just realized I didn't copy the full command properly. The reference file ~/mafa5. is missing its .fa, but I executed the command properly with .fa added to the reference path. I just didn't copy it from my command line properly.