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### Description of feature
Can sarek be used for variant calling in plant genome? And if possible, what should be done?
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Hello, in *LongPhase* paper, you utilized `minimap2` to align sequences to reference, and then performed variants calling using `PEPPER-WhatsHap-DeepVariant` pipeline. However, to my understanding, wh…
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Hi,
Thanks for developing this nice tool.
I have two genomes, assembly1 and assembly2. My goal is to use these two genomes as reference genomes, align reads to each of them, and call variants. T…
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Hi,
I would like to benchmark a method not included in your repository. Could you please advise how to use your code to do this? I would like to compare my caller to the callers in your benchmark.
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### Description of the bug
Hi am working with the pipeline, in the test working fine. with samples do not report the VARIANT_CALLING, there is no error in the run.
How I can make that processes?
##…
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Assignment instructions:
- [x] Align the reads to hg19 build 37 genome
- [x] Generate quality statistics from the fastq or bam file using your tool of choice.
- [x] Call variants for the regions in…
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### Tested versions
- Reproducible in: master (61598c5c88), 4.3, possibly all the way back to 3.3.
The code of interest was introduced in commit 221f5da85 on 2021-08-15.
I apologize for not includi…
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@edmundmiller and friends :)
this is a placeholder to collect ideas to realise additional tutorials on use-cases of sarek
Variant Calling is currently being integrated (http://lescai-teaching.github.i…
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Hi all, I am working on benchmarking variant calling tools and I am now simulating low and high coverage hifi reads for this purpose. But I am not sure whether my workflow is correct as I received mes…