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.
CombineGVCFs generate idx files way bigger that HaplotypeCaller
I used HaplotypeCaller in GVCF mode. The output g.vcf files came out with g.vcf.idx files. On the next step, I am using CombineGVCFs on the g.vcf files. The tool is regenerating the g.vcf.idx files. This is example warn message:
WARN 12:45:50,628 RMDTrackBuilder - Index file /path/to/sample1.g.vcf.idx is out of date (index older than input file), deleting and updating the index file.
My biggest worry is that the new idx file is way much bigger (the original was 166472 bytes and the new is 217546623 bytes! Is this ok?