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tgen / pegasusPipe

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vcf tools normalize creates 0 byte index file #26

Open tgenahmet opened 7 years ago

tgenahmet commented 7 years ago

NMTRC_C018_0037_ps201703031555.

A separate step to create index file on the vcf might be necessary.

PedalheadPHX commented 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

tgenahmet commented 7 years ago

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.

tgenahmet commented 7 years ago

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.