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
- 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?