Darren J. Lin

@molbio-dresden Thanks for your feedbacks. I found the legend in another file, but I suggest to have the legend in the dotplot figure.

Hi, I also mapped short-reads to the HPRC graphs and followed the ```augment```, ```pack``` and ```call``` pipeline for variant discovery. According to the above discussions, I still have the following...

@glennhickey Thanks for your quick response! I still have the following questions: 1. I mapped short-reads of Sample-A to the graph provided in the Science paper. This graph contains ~167,000...

@briannadon Hi, I also want to convert GAM to GAF, what's the full command of the conversion. I tried ```vg convert -G **.gam > **.gaf```, but it failed. Thanks!

@glennhickey Thanks!

Hi, What are the outputs in the log file, could please paste the last few lines. Moreover, please try without ```--graph```option and see what's going on.

The number of segments identified in the 10mb window was much more than the number identified in our data. Since SVision codes these identified segments as images, the unexpected large...

In the file chr1.segments.20.bed, the first column is the read name, you could go to the loci span by that read. Would please also send me the chr1.segments.20.bed file?

The ```chr1.segments.20.bed ``` file contains around 900 segments, but your log file showed that SVision writes 11170 segments to this file. I made a test on chr1 of sample HG00514...

For ```src/output_clusters.py```, please uncommented the code in line 91 and change it to ```logging.info('[Debug] Write {0} segments to: {1}'.format(len(all_segs), chr_segments_out_file)```. You could run SVision in your conda environment via ```python...