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**Describe the bug**
When trying to simulate desired insertions from VCF file, the insertions are not present in the resulting reads. Golden VCF file is completely empty after successful run (no muta…
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### Description of the bug
hi,i find
```
process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOTYPEGVCFS (joint_variant_calling)" going wrong.
…
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Hi,
Is that possible to add the alternative sequence in the VCF file?
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Can I use phased BAM and phased VCF files generated by Pepper-Margin-DeepVariant as inputs for dma anlaysis?
If this approach is successful, does it imply that the 'methyl_call_processor' and 'phase…
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Augur uses a variety of functions to read VCF files, including TreeTime's `read_vcf` which now includes a lot of validation and helpful error messages. We should shift all our VCF reading to use this …
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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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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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zeeev updated
2 months ago
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I am running bcftools +liftover to convert a vcf file generated with hg19 to hg38
Got these errors/warnings:
Merging 1466 temporary files
[E::hts_open_format] Failed to open file "TempDk63j4/01022.…
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Hi there,
I tried to run vamos on a long-read BAM file, with the following command:
`./vamos --read -b HG002.target.bam -r target_region.bed -s HG002 -o HG002.chr1.vcf`
When getting the output …
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I have an issue with successfully running the genebe commandline tool.
**input command:**
`genebe annotate --input 24072-01-01_split.vcf --output 24072-01-01_split_genebe.vcf --progress`
**erro…