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Hi,
In the output VCF of MC pipeline, there are a few duplicated variants after left-algin. Below is one example from the HPRC VCF:
Before left-align (`bcftools view -r chr22:15409352-15409435 h…
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Dear @readmanchiu,
The [Variant Call Format Specification v4.4. and v4.5](https://samtools.github.io/hts-specs/VCFv4.5.pdf) were released recently. One of the major changes is support for (short) t…
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Seems like this is the only filter without a clear and/or set message in Pd...
so... for the sake of consistency...
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Hello :)
Thank you for this software, it works fantastic!
I have a question about how I can extract a phased VCF file from the haplotagged bam file that I have created. The original VCF that the r…
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**What is your question?**
@eblerjana I am working on reconstructing a haploid haplotype using the imputed genotypes from PanGenie. Currently, I am using the following commands:
```bash
PanGenie …
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Hi @starskyzheng
I’m using PanPop under a Conda environment to merge structural variant (SV) VCF files. These VCF files had previously been merged using bcftools as I’m working with multiple sampl…
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Hi Jody,
I have just been running tbprofiler with some samples using VCF as the input (it is ONT data I have variant-called with Clair3). Forgive me if I have missed it somewhere but there doesn't …
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Hello, is there any way to get a vcf file for the merged and filtered regions, instead of xlsx file?
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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
latest
### Workflow Execution
Command line (Local)
### Other workflow execution
_No response_
### EPI2ME …
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Hi,
This is a great and very important tool, thank you for developing it !
Our entire pipeline is hg19 based, due to requirements from the clinicians.
Is there a way to upload VCF file from assemb…