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GenotypeGVCFs Error:

ChayanChayan Lund University, SwedenMember
edited January 2017 in Ask the GATK team

Hi, I was trying to run GenotypeGVCFs with my data as follwing (version GATK 3.7):

java -jar /var/bin/GenomeAnalysisTK.jar -T GenotypeGVCFs -R RefGenome.fa --variant a-45.g.vcf --variant a-8.g.vcf --variant e-18.g.vcf --variant e-55.g.vcf --variant e-69.g.vcf --variant e-854.g.vcf --variant e-98.g.vcf -stand_call_conf 30 -o 7samples.vcf

And I got an error like this:

The list of input alleles must contain as an allele but that is not the case at position 4988; please use the Haplotype Caller with gVCF output to generate appropriate records

But I have produced the *g.vcf files using the Haplotype Caller. Kindly correct me if I am wrong or give me an solution. Thank you.


Best Answer


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