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GATK version: gatk-4.2.3
I have two bam files: `Tumor.bam` is cfDNA data, and `Normal.bam` were reads from white blood cells.
There's a variant C to G at `chr7:116795782` (hg38), I can get this …
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Hello again!
I was able to run the script and everything was correct ! The problem that I face is that I trying to interprect was is the biological meaning of the correlation and rank values. Despit…
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I am trying to run Control-FREEC on a set of samples (WES) and I get segmentation faults in some of the samples while others complete fine.
```
..Annotation of CNVs for X
1 0.00875069
2 0.93584…
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Hi,
After some testing I am trying to download another instance of ITSFASTR so I can analyze real data. However, when I execute the code after having modified the samplesheet.csv and the config.yaml …
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Looking at a few cfDNA samples across different runs, we've noticed instances where the meth_qual distribution can vary widely quite a bit. Eg. some samples are strongly piled up near 0 or 255, and ot…
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I am running CNVkit using two options. First, I am using three samples as a reference and second, I am running it without any reference. However, in each case, the sex identified is opposite. How to d…
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I noticed some inconsistencies between public cBioPortal and MSK cBioPortal regarding structural variant data. I'm also not able to pull structural variant data anymore via the API endpoint for these …
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Thank you for the amazing toolbox! I have noted something odd in the scripts generated to run lofreq call by makeSomaticScrtipts.py
Running 'makeSomaticScripts.py single:
```
#!/usr/bin/bash
hom…
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