8000 Inquiry on Visualizing Variants with SplitThreader · Issue #126 · MariaNattestad/Ribbon · GitHub
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Inquiry on Visualizing Variants with SplitThreader #126

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Thena-Hu opened this issue Feb 6, 2025 · 1 comment
Open

Inquiry on Visualizing Variants with SplitThreader #126

Thena-Hu opened this issue Feb 6, 2025 · 1 comment

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@Thena-Hu
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Thena-Hu commented Feb 6, 2025

Hi Maria,

I would like to use SplitThreader to visualize detected variants. My BED file is derived from the analysis results of PacBio Human-WGS-WDL, which includes the mosdepth output (file size ~177MB). The command used for mosdepth is as follows:

mosdepth \
  --threads 3 \
  --by 500 \
  --no-per-base \
  --use-median \
  Sample.GRCh38 \
  /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/Case_5.GRCh38.bam

Additionally, the VCF.GZ file comes from the HiFiCNV analysis results (file size ~3.6KB). However, when using SplitThreader, I encountered the issue shown in the screenshot below. The error message on the right panel suggests that the BED file might be too large, leading to input failure.

Image

At the same time, I am uncertain whether setting a larger coverage parameter of mosdepth would filter out some variants, making them undetectable. I have not yet try to convert the VCF.GZ file into BEDPE format.

I would appreciate any suggestions on possible adjustments. Thank you for your help!

Best regards,
Thena
@MariaNattestad
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Don't worry, variants won't be filtered out due to setting a higher bin size in mosdepth. SplitThreader will still show all the variants in the VCF or BEDPE, regardless of what is going on in the coverage data. If you need to see anything more granular than you can see from the coverage, then that's when you go over to the Ribbon tab to see the actual read alignments.
I hope that helps! Let me know if you have any more questions :)

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@MariaNattestad @Thena-Hu
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