This adds a ##source=Sentieon row to the haplotyper output .vcf (by default) and allows the field value to be configurable by the pipeline through the key:
"HaplotyperVCFSourceField": "String"
It necessarily reindexes the vcf in the haplotyper stage since the header has been modified and there will be index mismatch errors in subsequent steps (VQSR).
This adds a ##source=Sentieon row to the haplotyper output .vcf (by default) and allows the field value to be configurable by the pipeline through the key:
"HaplotyperVCFSourceField": "String"It necessarily reindexes the vcf in the haplotyper stage since the header has been modified and there will be index mismatch errors in subsequent steps (VQSR).