about running variant calling ( final UnifiedGenotyper and HaplotypeCaller vcf files )

kimm55038kimm55038 south koreaMember
edited January 2017 in Ask the GATK team


I am currently having a hard time looking for a fatal error that considerably reduces the file size of the vcf files using UnifiedGenotyper and HaplotypeCaller process. (there is a huge difference in the number of lines if I open the vcf files via typing 'vi')

From indexing a fasta file, using samtools faidx, and creating .dict file to using picard and gatk, I haven't gotten any warning or error messages. I have installed the required softwares without any error. No problem with running them, too.

The correct file sizes should be about 11MB for UG and 7MB for HC, but all I get is 7MB and 6MB each.

I attached a word document that has all my command lines in it. I've reinstalled all the necessary software (bwa, samtools, picard.tar + picard-tools.zip, gatk) and ran the whole thing twice changing the home directory of my processing. Can you please take a look at it? Thanks.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Hi there, we don't have enough information to answer you. Please post your command lines in plain text rather than as an attachment. Also, please post the log output of the step that you think is failing, and explain what is the basis of the "correct" file size.
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