Darren J. Lin
Darren J. Lin
Hi Fritz, I am using the compMUMMer function to evaluate the breakpoint accuracy of callers. In the source code, I found the tag "**_EUR_AF_**" is taken to update the variable...
**1. What were you trying to do?** Calling SVs from an augmentation graph. **2. What did you want to happen?** Get novel SVs from the augmentation graph. **3. What actually...
Dear author, I am trying to phase SVs with HP added BAM files. The command I use is ```sniffles --phase```, other parameters are just default. In the output, I found...
Dear author, I go through SupplementaryData.pdf and found the example of using .gff3 to annotate the plot. But how can I add the figure legend, I did not see the...
Dear vg team, I read the recent HPRC publication 'A draft human pangenome reference'. Inspired by this paper, I tried to call SVs only belongs to sample A but absent...
Hi, I am detecting SVs from the HG002 assemblies using PAV and SVIM-asm. The HG002 assembly was aligned with minimap2 and lra. PAV worked fine on both mapper aligned assemblies,...
Hi Tobias, I am using delly to call CNV from long-read data with the command below: ``` delly cnv -u -z 100000 -o $out/tumor.bcf -l $vcf -c $out/tumor.cov.gz -g $ref...
Dear developer, I want to convert the GAM to BAM format via VG surject command, but it failed because of the different attributes between GraphAligner and vg aligner. The differences...
Dear author, I am trying to merge SVs detected from assemblies and reads. Here is one call from assemblies: Here is another call from reads: The merge command is: ```...
Dear author, Firstly, I got 22 ```sfs``` files after running ```SVDSS search --index ./hg38.fmd --workdir ./HG00733/ --bam HG00733/smoothed.selective.bam```. Each of the ```sfs`` file is named as ```solution_batch_*.sfs``` and contains some...