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I have a folder with ~12 vcf files from human genome ONT data that I want to plot, but I get this error: ValueError: Image size of 1358933x7111 pixels is too large. It must be less than 2^16 in each d…
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The --tab output is a great way to visualize annotated variants, especially due to multiple lines used to represent overlapping transcripts, genes, features, etc, and the many options to control this …
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For many downstream analysis it would be nice to also publish the VCF files with the ref/alternate allele and the frequencies.
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The [VCF 4.4 spec](https://samtools.github.io/hts-specs/VCFv4.4.pdf) now allows for an initial symbol indicating the phasing of the first allele. For example, `/0/1` is a valid genotype. At present, v…
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Hi,
```
version: v3.0.1
Files and parameters used:
-e 3000000000
-k 31
-o index/processed
-r chm13v2.0.fa
-t 10
-v merged.sorted.multi.vcf
Determine allele se…
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This is the command that I used for SNP calling
bcftools mpileup -f reference.fa alignments.bam | bcftools call -mv -Ov -o SNP_calling.vcf
This is an example of the output
Chr1 271 . G GAAATAGCATA…
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Hello,
I am attempting to use MMARGE for analyzing ATAC-seq data from different strains of mice. I downloaded the SNP and Indel vcf files from the Mouse Genomes Project website and sorted them usin…
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bcftools sort exits with the error below. I tested the same sort on all the input files eliminating the possibility that the inputs are problematic.
1. Jasmine is not constructing a valid header
…
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## Describe the issue
Hi. I am currently using VEP v111.0 to annotate my vcf files. When I use --offline mode and provided the synonyms file, errors shows up and some of the chromosomes do not overla…
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## Bug Report
### Affected tool(s)
_Tool name(s), special parameters?_
RenameSampleInVcf
### Affected version(s)
- [ ] Latest public release version [version?]
- [ ] Latest development/maste…