VCF output from GBS de novo is truncated

NGSEP / NGSEPcore

NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions, deletions, and genomic regions with copy number variation (CNVs).

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VCF output from GBS de novo is truncated #38

Closed edgardomortiz closed 2 years ago

edgardomortiz commented 2 years ago

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 commented 2 years ago

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