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Folks occasionally but consistently ask for this information on the forum and our current answer is that we provide these files as is. For the new GATK4 documentation, which we plan on releasing on Ja…
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Hi,
This is a really great tool and works very fast, thanks!
We've been trying it out in different ways and many times the resulting phased VCF files contain multiple lines of headers in the middle …
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**1. What were you trying to do?**
Understand the output VCF of ```vg call```
**2. What did you want to happen?**
Analyse VCF file, first retrieve which kind of variant is present in each po…
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Hi,
We are currently using the VEP v111 Docker container to annotate VCF files. However, we are facing the following issues:
1. Performance Issue: Annotation of a very small sample VCF file takes…
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Idea pitched by @ViktorHy
Is possibly equally fast and we avoid having to maintain fastgnomad.
Related issue #261
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Dear Giovanni,
Thank you for your nice software. I am using scAllele for the detection and analysis of variants using scRNA-seq. I wonder how you get the information about 0/1 or 1/1 in Figure 2E of …
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**1. What were you trying to do?**
calling structural variation after mapping long-read data on whole genome pangenome graph
**2. What did you want to happen?**
create a VCF file which contai…
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### Is your feature request related to a problem? Please describe
If we take as example the bamtools, samtools and bcftools the output channel are inconsistent.
- BAMTOOLS_CONVERT:
```groovy
out…
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Thank you very much for your research in the field of CNA analysis. I have encountered some issues while using CalicoST. When I executed cellsnp-lite with three samples (10x Genomics Visium v2), the o…
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I am currently running vcf2circos on a conda environment; installed from https://anaconda.org/bioconda/vcf2circos.
The data is run through GATK pre-processing and then using Manta as a variant caller…