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I am trying to understand how selscan excludes variants, as a region I am interested in appears to be missing some important variants in my output. My command is:
selscan --ihs --vcf inFile.vcf.gz…
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**Describe the bug**
When clicking "show reads", the IGV header appears but the variant coordinates are not automatically populated in the search field. Even if I manually enter coordinates, read dat…
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hi
I am having difficulties running the tool and get the output. The analysis skips all the variants for a gene and doesn't give out any results. Do you know what is wrong with the input ?
Thank…
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Hello,
I have a dataset with both common and rare variants. Is there a way to simultaneously test them both?
How exactly is the grouping data for rare variants formatted?
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Hi, i have the same problem.
I want to perform rare variants (MAF < 1%) analysis in Regenie, and have tried many times to follow your earlier advice to others, but still encounter the s…
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Hi,
There seem to be a problem with running the following script below when I apply a --freqUpper filter of 0.01 or 0.05. The script would run without a problem when the --freqUpper is set to 1 (equ…
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We need to create some mondo subset files for use in KGs along the following lines:
- Rare disease subset
- Rare disease subset with leaf nodes representing variants in same gene rolled up to pare…
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![image](https://user-images.githubusercontent.com/59941517/173229604-dc487768-ac7d-45ab-8ee9-b8d7c18449a3.png)
This ad uses the type 8, but on my frontend, the description is none and the image were…
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Hi!
I want to create the mask with variants from different chromosomes (pathway-based rare variants association). I've found in one of the closed issues the GENPOS in the variants set file doesn't af…
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Using sniffles 2.4 in merge mode on chm13 produced an invalid variant.
This isn't a huge problem because most vcf parsers can handle the error plus SVs at the beginning of chromosomes should be a …