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.
What means is " * " in alternative allele ?
I ran HaplotypeCaller about multi-samples to obtain gvcf and combined multi-samples's gvcf using GenotypeGVCF.
As result of GenotypeGVCF, I obtain joint,vcf.
However, I couldn't understand contents in my joint.vcf,
10 134767 rs12768206 A G,* 11674.12 . AC=30,4;AF=0.246,0.033;AN=122;BaseQRankSum=-1.260e+00;ClippingRankSum=0.458;DB;DP=1662;FS=1.110;InbreedingCoe
What means is " * " in alternative allele column and What is genotype?