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# problem in UnifiedGenotyper

BostonMember Posts: 76
edited October 2013

I run the UnifiedGenotyper with 3 samples. After almost 4 hours I got the following ERROR. What is this error mean? How I can to fix the problem? Thanks

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-4-g4a174fb):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR
ERROR MESSAGE: -1 does not represent a valid base character

Post edited by Geraldine_VdAuwera on

Hi Mahyar,

Can you please post the full stack trace? The stack trace is the part of the console output that details the problem, just before the ERROR block.

Geraldine Van der Auwera, PhD

• BostonMember Posts: 76

Hi Geraldine,
Unfortunately, I deleted the log file.

Then I'm afraid you'll have to re-run it. Try running with -l DEBUG`, it will give more information about what is wrong. Be sure to save the log file, as I can't do anything without that information.

Geraldine Van der Auwera, PhD

• BostonMember Posts: 76

Hi Geraldine,
I run the UnifiedGenotyper for my all 42 samples and I got the VCF file for all sites. In the 4th column of the VCF file I have QUAL-value which is range between 0 to 25000. What would be the threshold of selection QUAL. (e.g. 50, 100, 1000, etc). Please advise>thanks

Geraldine Van der Auwera, PhD

• BostonMember Posts: 76

Hi Gerladine, I Used "HaplotypeCaller" for calling variant of one of my Bam file. However, after 3 hours it created the VCF file, but there is no information in the file and just heading. In below, you can see my commands: What is wrong? please advise, Thanks

java -jar GenomeAnalysisTK-2.2-4/GenomeAnalysisTK.jar
-R ucsc.hg19.fasta
-T HaplotypeCaller
-I 15V_post_reorder_GROUP.rg.bam
--dbsnp dbsnp_137.hg19.vcf
-gt_mode GENOTYPE_GIVEN_ALLELES
-out_mode EMIT_ALL_SITES
--out 15V_post_afterQC.vcf