VCF output from GBS de novo is truncated

[edgardomortiz]

I am having the problem that the last line of my VCFs files always has fewer samples than the rest, so I don't know if only the last line is affected or if the file is missing a portion. Checking the consensus.fa it would seem that some loci are missing from the final VCF. How can I assure to get the full VCF?

I am using the GUI in Ubuntu, NGSEP 4.1.0

Thanks

[jduitama]

Hi Edgardo

Sorry for the late answer. This normally happens when the process is cancelled or the disk is full. Please share with me the log to see if the process finished or if an error was reported

Jorge