Hi,
After supplying CRISP with a bamfile list which contains PS= the output VCF says that it is VCF format 4.0
This has prevented picard update sequence dictionary from running correctly as it requires a GT field in versions prior to 4.1.
The fix was editing the VCF format line in the crisp VCFs to be ##fileformat=VCFv4.2
Hi, After supplying CRISP with a bamfile list which contains PS= the output VCF says that it is VCF format 4.0 This has prevented picard update sequence dictionary from running correctly as it requires a GT field in versions prior to 4.1. The fix was editing the VCF format line in the crisp VCFs to be ##fileformat=VCFv4.2
Just thought I'd flag that for you