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The header line for `GATKCommandLine` causes problems:
```
##GATKCommandLine=
```
Calling `readVcf` gives me:
```r
fl
LTLA updated
10 months ago
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hello,
when I ran the following code, I got this error:
Error in textConnection("sout", "w", local = TRUE) :
all connections are in use Calls: Motif ... tryCatchList -> tryCatchOne -> doT…
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I am running IMSindel in HPC However the analysis didn't finish for more than 24h
the command:
IMSindel/bin/imsindel --bam APS14.downsampled.bam --chr chr7 --outd chr7_del_out --indelsize 10000…
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**Snakemake version** 8.16
**Describe the bug**
When using `--sdm conda apptainer` on an HPC system, snakemake fails to create log files when they are given as captured stderr output.
*…
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we need to define module-specific thresholds triggering potential warnings or errors.
pdp10 updated
6 years ago
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- Cutadapt and Python version used: 4.8
- The method you used to install the tool (conda or pip, for example): Used mamba
- The command-line parameters you used for demultiplexing paired-end reads w…
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Hi @ydLiu-HIT, I am trying to run the variant calling using multiple threads using this script,
```
#!/bin/bash
set -e
# Constants and paths
REFERENCE_GENOME="/Data/dataflash/Benchmarking/hs3…
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Hi,
In recent samples analyzed with v3.5.5, we see very high indel burdens.
I found several examples of indels that overlap the NOISE mask, but were not filtered out - they still show up with FILT…
gevro updated
4 months ago
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Hi,
I've using the bam_readcount wrapper "mgibio/bam_readcount_helper-cwl". The output files (snv or indel) contain control characters which cannot be processed by the vcf_readcount_annotator.
W…