Open tgenahmet opened 7 years ago
Is this a common error? Also is it occuring as part of the process, not sure if we can turn it off or not
No it's not common. Haven't totally figured it out yet.. It crashes GATK downstream as usual which can't automatically figure out the type of the file when it is 0 bytes.
A very simple solution is to remove the *idx file so GATK can internally create one for itself rather trying to use the 0 byte idx file. It worked on the sample that was failing because of this.
NMTRC_C018_0037_ps201703031555.
A separate step to create index file on the vcf might be necessary.