I am using GATK 2.7.2. I am working on the Best practices of GATK. I have followed all the steps as mentioned for Best practices. All the .vcf files that are needed as input are downloaded from ftp bundle/2.3/h37.
In Variant Recalibration step: I am using HaplotypeCaller tool to generate the raw_variants.vcf The .vcf is generated but it consist of only headers and no variants for the same. Due to this issue the VarianRecalibration tool is not working as it needs annotation.
I am attaching the raw_variants.vcf that is generated after executing HaplotypeCaller tool.
I have one more question: Whether the HaplotypeCaller adds quality score in the output .vcf file?