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I have a vcf file for one sample. I ran "bcftools stats -s - -F ref.fa variant.bcf.gz > variant.vcf.stats".
I am not sure what the problem is. Could anyone please help me out?
In variant.vcf.stats…
wul88 updated
4 years ago
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Hello,
I am using BCFtools 1.10.2-GCC-9.2.0 and trying to execute the following command:
plot-vcfstats -p ${outFolder} ${fileName}.stats
and this gives me the following error message:
Plo…
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Hello,
Similar to issue #1171, when trying to compile bcftools from a github clone on macos (my vers: 10.13.6 High Sierra), bcftools fails to compile. This is due to an issue with enabling perl fil…
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Hello! I am trying to understand how the program calculates the number of nHet and nHomA sites. I really tried looking at the script, but I need some help understanding the code.
I know the header …
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I downloaded cache files from ensemblgenomes which does not contain sift/polyphen scores. The info.txt files in the cache directory does not contain sift b or polyphen b. How do I generate those score…
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I am trying to install bcftools to access the `bgzip` command in order to use the Michigan Imputation server. However, following the installation instructions give an error which I'm not sure how to s…
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Hi There
I am using tibanna version 0.16.0
I have a WDL workflow I'm running on my regular compute resources and I wanted to test it on tibanna. After setting up the input JSON with inputs I ran …
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hi,
When I run the command:
seqmule download -down hg19all
it cannot download the databases, some parts are missing (it should be 5.2 gb but it is 1.6 gb somehow)
Either it gives the error: ther…
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Hello, trying to compile the latest version from github and running into this
```
vcffilter.c: In function ‘main_vcffilter’:
vcffilter.c:477:90: error: ‘VCF_OVERLAP’ undeclared (first use in this…
ghost updated
4 years ago
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When I run plot-vcfstats, there's an error with the version of python that's being used. Here's the output.
```$ plot-vcfstats -p study.plots study.vcf.stats
Parsing bcftools stats output: study.v…