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--Hi,
runnning:
ngscat2 --bams ./SRR6823381.bam --bed ./Exome-Agilent.bed --out /work/ngscat --reference ./Homo_sapiens_hg38.fasta
it failed with:
Traceback (most recent call last):
File…
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### Description of the bug
Manta fails with a path error:
```
error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-16 03:00:07.184 [Actor Thread 16] ERROR nextflow.processo…
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Hello,
I am using the program to estimate the PCR duplicates in exome seq data. However, the first code run smoothly. The second is not running I would say due to problem with python interpreter. I …
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Hello,
Thank you for developing Manta.
I am trying to merge SVs from different callers (Manta, Lumpy, Delly, Clever).
I was just wondering if keeping calls with only PASS filter is sensible to…
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Hi
I am having issues installing this:
Below is the error I am _encountering
> if [ ! -e ../obj ] ; then mkdir ../obj ; fi ; \
> if [ ! -e ../bin ] ; then mkdir ../bin ; fi ; \
> cd ../obj; \
…
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For the sake of pulling in relevant meta data, I suggest to use CSV/TSV as default input format rather than a folder with a bunch of FastQ files.
Suggested format would be:
```
IndivID;SampleID…
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Hello, I am trying to install ExomeDepth (`install_github("vplagnol/ExomeDepth")`) in order to install and use DECoN but unfortunately, it is not working.
I use the R version 4.2.1
Does anyone al…
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Hello,
I had attempted to run DRUMMER using the exome mode across my genome reads as follows:
```
mkdir -p /rhea/scratch/brussel/vo/000/bvo00030/vsc11010/results_mouse_debugging/drummer/
mkd…
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Interested if people thinks this makes sense, and how much work it would entail.
For the pt189 analysis, I'd like to view pileups for an arbitrary set of BAMs (normal exome, plus multiple somatic exo…
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The header line for `GATKCommandLine` causes problems:
```
##GATKCommandLine=
```
Calling `readVcf` gives me:
```r
fl
LTLA updated
8 months ago