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Is there a way to generate a joint-genotyped vcf with pangenie? If I understand the software correctly, only the variants in the pangenome reference are called across all the genotyped samples while…
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Hi,
Thank you for your excellent pipeline. I utilized a custom-made VCF file for genotyping. However, some variations were identified during the genotyping step.
here are some examples:
[屏幕截图 202…
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Hi there,
I would like to use QuantiSNP to call CNVs from my genotyping SNP array but I cannot install it without the .exe file.
Could you please update the repository so the file can be download…
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Hi there,
I have a question regarding genotyping GVCFs that were generated from other vendors.
For example, can I use GVCFs from Sentieon to jointly genotype variants using GLNexus?
What imp…
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Hi,
I am trying to use PanGenie to genotype personalized minigraph-cactus graphs generated by `vg haplotypes`. In the [personalized pangenome paper](https://www.biorxiv.org/content/10.1101/2023.12.…
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Hi,
After running `BayesTyper genotype`, the output vcf file added `*` allele to the `ALT` field.
For example:
This is the input record, the `ALT` field only contains `T` allele :
1 11…
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Hello,
I find there are a fewer SNP overlap rate between the callset form pangenome-graph-from-assemblies and the GATK results. What could be the reason? The article seems to only compare the abili…
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Expected Behavior
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Create a generic data file parser that could be used with all of the file upload functions that will s…
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Hi,
Can I use CAPG to genotype whole genome instead of some "targeted genomic regions", how to do that if I can?
Best,
Kun
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One of the really nice features of `vcf2vcf` is the genotyping feature. I don't know any other software that really has this capability. I've tried using `freebayes` force-calling which is very fast b…