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.
size of gvcf generated by Haplotypecaller of 30x and 100x coverage of the same sample are different
I have a RAW reads with 30x and 100x coverage. When I followed all pre-processed steps as mentioned in GATK best practices to call variant. At last, gvcf files have been generated from both data by Haplotypecaller of GATK 4 but file size different. Why size of gvcf files are different, even same reference sequence was used in alignment by BWA mem? I think size of both gvcf files should be same if variants have been called by using same reference, same aligner i.e. BWA-mem with default parameters for both samples and same per-process steps were followed.