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Bringing in the below questions from #363, which were off-topic for the containing issue but worth discussing:
>What is the artificial (or generally acceptable) boundary between CNV versus tandem r…
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## Goal:
- What proportion of variants and which ones show a signal relative to their WT?
## Basic Analysis using mean profiles:
- Using correlation coefficients (by Marzieh)
- [x] Replica…
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--Hi,
i can't detect short CNV. Is there a way to improve the detection ?
I use these parameters:
Rscript $PURECN/PureCN.R --out $OUTPUTS/$lib --tumor $OUTPUTS/${lib}"_recalibrated_coverage_lo…
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Now #56 is done do we want to be able to constrain by multiple phenotype conditions?
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Dear developer,
Thank you for providing this wonderful tool! I am wondering about the compatibility of individual-level gVCF files obtained through GATK4 with DeepVariant for joint calling of multi…
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I am seeing something I did not expect and wondering if this is the expected behavior. It is related to the ‘repeatSubunitLength’ property of the ReferenceLengthExpression. I am generating VRS objec…
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Thank you for providing an example to find sequence_locations such as dbSNP IDs for a given gene and allele at https://github.com/cpicpgx/cpic-data/wiki#allele (e.g. CYP2D6*3).
In practice, users w…
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### Due date for Sprint 11 - May 16th.
### General
- [x] Improve installation instructions so that the annotator can be installed without issue on Amazon Linux 2023 - @dlin30 - 2024/05/08
### Prote…
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Hello Xiaofei,
Thank you for developing the Haphic software.
I am currently working on the assembly of a complex polyploid genome and I am trying to scaffold the “p_utg” sequences obtained from …
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Hello, I want to ask what are the input files of 'imputed', 'andres', 'inv17_h1h2', 'mathieson' in config? Thank you!