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.

missing calls from VCF

1. I combined gVCFs of ~100 individuals. However, when I open the file there are missing genotypes. i.e.- not all rows have equal number of genotypes (see attached). I am using GATK_3.4.6 and the command I am using to merge the gVCFs is:
$cmd = "java -Xmx4g -jar $GATKdir/GenomeAnalysisTK.jar -T GenotypeGVCFs -R $genome --dbsnp $ResourcesDir/dbsnp_138.b37.vcf $filesToJoin -o example.vcf";

Where $filesToJoin is a string with -V individual.gvcf

  1. The total number of individuals is 400, and I combined every 100 together. Can I do the calibration with several -input arguments or must I merge all merged files into one?


Sign In or Register to comment.