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Hello, I was using GATK4 LiftoverVcf to adjust the coordinates of variants in my vcf4.2 file (created by plink1.9) to hg38 reference build. However, I got this error:
The provided VCF file is malfo…
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When I run the commands
``` bash
vcftools.0.1.14 --vcf test.vcf --out test --recode-bcf
bcftools-1.3.1 view test.recode.bcf
```
bcftools dies with a segfault. This file `test.vcf` contains
```
##f…
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```
Traceback (most recent call last):
File "/home/theo/anaconda3/bin/vcftoolz", line 8, in
sys.exit(main())
File "/home/theo/anaconda3/lib/python3.9/site-packages/vcftoolz/cli.py", line …
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- [ ] add_value > tools/add_value
- [ ] analyze_covariates > tool_collections/gatk/analyze_covariates
- [ ] annotation_profiler > tools/annotation_profiler
- [x] bamleftalign > tools/freebayes
- [x] b…
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### Description of the bug
How can I use a custom snpeff reference database, such as candida.auris, in Sarek. This snpeff reference did not included in Sarek. I tried --snpeff_cache, but not work.
C…
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I'm getting the error Error in count.temp[, 2] : subscript out of bounds
while doing GWAS with InDel data. The updates don't seem to be helping. How should the input hapmap data look like to not g…
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Hi I'm trying to download vcftools via git clone and I keep getting this weird syntax error whenever I get to the `./configure` step:
```./configure~: line 1: syntax error near unexpected token `('…
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I have a problem with the Vcftools installation.
When I run "make" I get the following error:
./configure: line 4636: syntax error near unexpected token `ZLIB,'
./configure: line 4636: `PKG_CHEC…
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Hi,
While using vcftools for window-pi analysis, I found in the output, the number of N_VAEIANTS is different with my input VCF files. And here is my command:
`vcftools_0.1.13/bin/vcftools --vcf chr…
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### Description of the bug
Hi, I'm trying to use Sarek from the annotation step. I'm using Linux and Conda. Each time I try, it gives me an error like this:
ERROR ~ Error executing process > 'NFCO…