If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.