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Hello, I followed the installation instructions by using `pip -U install` and the command `vcfstats` is still not recognized. When I ran the installation command I got no errors. Do I have to clone t…
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### What happened?
Trying to call variants on a WGS BAM file generated from `minimap2` using this command:
```
nextflow run epi2me-labs/wf-human-variation \
-w output/workspace \
-profi…
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Hi there,
I was trying to produce plots with vcfstats and it doesn't seem to represent MNPs (multiple nucleotide polymorphisms) as reported by bcftools stats ?
I also notice a discrepancy in SNPs/…
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The vcfstats are able to produce a plenty of informative plots to explore and access genotypes in the vcf file. I'd like to list several currently not supported by vcfstats plotting possibilities whic…
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We're looking at ~700bp inserts using PacBio HiFi data using bcftools and we noticed some large indels (>100 or so bp) missing from the callset. I think this is due to the indel window size here
htt…
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Hi,
I am trying to plot the data from a vcf file I have. I used bcftools stats to produce a stats file and when I run "plot-vcfstats Phased_vcf.stats -p VCF_plots" I get the following error:
`…
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I tried to install from github repo, but got the below error (I omitted the earlier install outputs as I assume they wont be relevant for the error below).
I am installing on linux within condaenv w…
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I'm seeing a really awkward behaviour while installing `cyvcf2==0.30.1` (and even with earlier versions, depending on the host).
To reproduce the issue, using `docker`:
```bash
mkdir cytest
cd c…
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Hi,
Thank you for developing vcfstats software! Could you advise me please, where i may find the "config.toml" file to run vcfstats?
Regards,
Denis
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### What happened?
Hi,
I provided a ubam with Ml and MM tags to the workflow but get an error with sniffles2 which i think is because it did not perform alignment. Should it not start with alignin…