The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?