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Expected Behavior
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In the List Manager:
- You can create a list of type "genotyping_trials" - are these genotyping pro…
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Expected Behavior
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For Bugs:
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### Environment
#### Steps to Reproduce
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**1. What were you trying to do?**
After building a plant graph pan-genome of with Minigraph-cactus, I used vg to map short reads to graph and genotype.
Details are as following link (Part 4: G…
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Following on from #343
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### Summary / Overview
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- 4368d8a6 use a range 0-0.5 for MAF in the GUI
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- [x] [2-4H/3H] use --max-af for ! mafUpper, instead of --min-af
d935c6a8 appl…
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Dear developers,
I have 18 samples in my project and it seems GATK starts once a few alignments (bam files) are ready.
Is it possible to start the GATK (variants calling) once all the alignmen…
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Hi, when I running the smc step, I find there are some warnings in the 'smc_out.vcftool.log' file.
$ grep "arning" smc_out.vcftool.log
Warning: Input is unsorted, results may not be complete.
War…
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### Ask away!
I'm trying to optimize the CNV bin size to find known mutations across several samples (mapped to hg19). I've decreased the bin size from the default, to 100, 10, 5 and 1kb. As I de…
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Hi everyone,
Im trying to get started with eager and I found this problem, in fact Im brand new with nf-core pipelines and I dont know if this issue is easily fixable. I recently installed nextflo…
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Hi Thierry,
I'm running into similar issues as the people who opened https://github.com/thierrygosselin/radiator/issues/183
I exported a VCF from STACKS 2 that was unfiltered and wanted to test …
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This issue serves as a discussion hub for development around a pipeline for benchmarking SVs. Development currently is happening on the [rm_benchmark_svs](https://github.com/broadinstitute/palantir-wo…