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I do not see anything in the docs (`GT_Pro optimize` help docs, the repo README, or [Shi et al., 2023](https://doi.org/10.1016/j.xpro.2022.101964)) on handling paired-end reads.
How should one han…
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hello,
thank you for this potentially useful tool. I have it running on delly output (bcf file) that had been filtered with the delly somatic filter. The file contains several SVTYPEs, namely DEL, DU…
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Hi,
I used Sniffles2 to generate a VCF file from 3 samples with ONT reads. When I look at the REF allele column, I found that they are all represented by N. I am wondering is there a particular re…
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We have entities like Sample and Assay which have records representing multiples specimens. Plan D involves doing things like incorporating weighted means into our repertoire of stats, but that will o…
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**Describe the bug**
Minimise the number of experiment checklists, to reduce confusion e.g. why WGS and genomic?
**To Reproduce**
**Expected behavior**
**Screenshots**
**Desktop (please…
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### Description of feature
The scatter count should scale with the family size to account for the multiple variants found per individual
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It's important to try and clear up some of the confusion. Here's one:
https://doi.org/10.1016/j.tig.2019.12.008
> Notably, tsinfer does not explicitly infer an ARG but rather a sequence of loca…
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Hello,
I have a question about how the VDJs are assigned to the contigs.
I have a trust4_cdr3.out, and I can see for example for malignant cells in my data, there are multiple VDJs. How is this po…
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I am running >20k Salmonella genomes with AMRfinder using the "--plus" switch and "-O Salmonella". In about 1% of the samples it will crash once the BLASTN starts for the point mutation search; if I r…
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The scatter_count parameter, used to control chunking for the genotyping stage, is currently hardcoded to 50. We should expose this as a configurable parameter, as we may want to adjust this for proce…