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For QuantStudio _Genotyping_ experiments as in [appbio_quantstudio_example03.txt](https://github.com/Benchling-Open-Source/allotropy/blob/main/tests/parsers/appbio_quantstudio/testdata/appbio_quantstu…
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**Describe the bug**
```
mgatk tenx -i DOGMA_sample1_exp1_libA/outs/possorted_bam.bam -n sample -o DOGMA_sample1_exp1_libA/mgatk/ -c 8 -bt CB -b DOGMA_sample1_exp1_libA/outs/filtered_peak_bc_matri…
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Note: This was also sent to Clement via e-mail. Then I realized I should ask through here instead. Sorry for the duplication.
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I saw your GraffiTE package a f…
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Sometimes in variant calling, it's necessary to force genotype all known sites regardless if a variant is found. Illumina has it:
- https://support.illumina.com/content/dam/illumina-support/help/Il…
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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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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,
Thanks for the great tool.
I am running the mtDNA genotyping viginette on one multiple myeloma sample that is originally a Multiome (GEX + ATAC)
This is the variants plot I get: (notice t…
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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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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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Expected Behavior
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In the List Manager:
- You can create a list of type "genotyping_trials" - are these genotyping pro…