Omar Abou Saada

The issue isn't glaringly obvious to me. Could you also send me your log file in the /Logs folder that should have been created? It should have some lines that...

I received the log file. The issue is that the illumina reads were mapped to a different reference than the reference given to nPhase, and the two references didn't have...

That's odd, maybe the --threads argument isn't being passed properly? I'm not sure what's causing this. The quickest solution, I think, is you can avoid running GATK through nPhase by...

nPhase only uses the short reads into to obtain a VCF with high-confidence variant positions, MarkDuplicates (and any filtering steps you wish to perform) is fine. I think they would...

Hi Elsa, For my paper I did just subset the data. In order for you to also run nPhase on one chromosome at a time you can simply separate your...

I'm glad you find nPhase useful! There's no function to turn nPhase results into a VCF or tag the long reads of a BAM file with a haplotype directly. It...

Hi Elsa, nPhase partial requires a sorted sam file, not a bam file, since my code reads the individual lines and I didn't use a library that can parse the...

nPhase doesn't output haplotagged BAM files but it does output a fastQ file for each predicted haplotig, so you could still assemble the long reads this way, but I can...

Hi Adam, Sorry for the delays in responses, I'm still not sure how you plan to cluster the tracks together so it's a little difficult to anticipate what sort of...

Nice catch! There are probably a few other errors that can be caused by the same edge case. I'll fix it for the next update