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I have assembled a bacterial genome from Nanopore long reads using Flye and would like to use polca to polish them using the Illumina paired short reads. I have installed Masurca by cloning from githu…
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According to the investigation of OOM(https://github.com/icgc-argo/workflow-roadmap/issues/136), we will implement the re-try mechanism for Sanger wgs variant calling step as what Alex suggested.
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Github:
https://github.com/Rbbt-Workflows/ARGOVarCall
Awaiting Miguel for docker image.
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Hello,
I am running into an issue with multisample calling for BND variants. I am merging two samples together.
Both of the following lines are in the multisample vcf, even though they correspo…
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Is there a way to use vg call with multiple file inputs? (i.e., vg call -v SAMPLE1.aug_graph.vg,SAMPLE2.aug_graph.vg,SAMPE3.aug_graph.vg -s SAMPLE1.aug_graph.support....)
I am attempting to look f…
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I feel there must be an easy answer to this query but I am unable to see it at present.
I am attempting to create a graph (currently with just two genomes) and then use the graph to create a vcf fi…
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I have been trying to use vg call to call variants from a whole genome graph. I have attempted to use vg call on the whole genome without chunking, but the output vcf file was empty. I then tried usin…
ghost updated
5 years ago
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Implement PoN code into Variant Calling
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Hello
Thank you for this great tool.
I am trying to call TE insertions on a tree genome which is ~ 830 Mb.
My config.yaml file is as follows:
```
# all path can be relatif or absolute
D…