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GenotypeGVCFs throwing this error: ##### ERROR MESSAGE: Invalid argument value ' ' at position 22.

dkcrossmdkcrossm Member
edited April 2014 in Ask the GATK team

Hello all!

I've been using GATK v3.1-1 for the last week or so. I've come across an error when I try and perform the Joint Genotyping on 5 different samples (family members). All 5 samples were processed through individually (following the Best Practices Guide) and the HaplotypeCaller was run in the gVCF mode. When I run GenotypeGVCFs I receive this error:

ERROR MESSAGE: Invalid argument value ' ' at position 22.

I'm not quite sure what to make of it because other projects with the same type of family size don't throw this error. Do you all know what it is referring to? I've even tried the nightly build (GenomeAnalysisTK-nightly-2014-04-14-g744780d) to see if that fixed the problem and it didn't. Here is my script:

java \
-Xmx22g \
    -Djava.io.tmpdir=$TEMP \
-jar /home/dkcrossm/tools/$GATK_DIR/GenomeAnalysisTK.jar \
-R $REF_FASTA.fa \
-T GenotypeGVCFs \
-ped $PEDIGREE \
-nt 4 \
--variant $SAMPLE1.hc.gvcf.vcf \
--variant $SAMPLE2.hc.gvcf.vcf \
--variant $SAMPLE3.hc.gvcf.vcf \
--variant $SAMPLE4.hc.gvcf.vcf \
--variant $SAMPLE5.hc.gvcf.vcf \
-o $SAMPLE.raw.snps.indels.vcf \
--dbsnp $DBSNP \    

I am also seeing this in a 16 sample run as well, but the position is 44 in this instance instead of 22. Any suggestions as to what it could be referring to? Let me know if you need anything else!

Thanks,
David

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