Monitor Progress of Haplotype Caller
Hello, we have a GATK automatic pipeline all set up. We noticed a run that looked finished but then noticed that some SNP/InDel calls were missing. We were able to see that Haplotype Caller died unexpectedly. It's progress meter only said it had finished a little more than 16%. The pipeline continued to process on this incomplete vcf file.
Am I correct in assuming that the only way we'd ever be able automatically note this error is if we monitor the progress meter of Haplotype caller because the vcf is being written as we go? Is there any way to write the vcf all at once at the end? This doesn't seem like a great idea anyway because of resource issues, but I am just curious. We cannot depend solely on the existence of an output vcf file unless this is the last step in the process. Is there any phrase we can monitor for at the end of the Haplotype caller that we can be sure won't appear elsewhere in the file? Like, "Done", "Finished", etc? Thank you!