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Request: Help with Obtaining STAR Alleles from VCF Files (Illumina Short Read Sequencing, Dragen Variant Caller)
Hi,
I’m looking to get STAR alleles for a set of VCF files generated from Illumina …
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Hi,
I'm doing an allele-specific analysis, the pipeline went well until the final ice-normalization step. Tracing backwards I found the raw matrics were empty, and markAllelicStatus aberrantly assign…
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### Installation Type
Docker
### pVACtools Version / Docker Image
Docker container, version 4.4.1
### Python Version
_No response_
### Operating System
_No response_
### Descri…
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Is it possible to make an allele-specific map with for genomes with ploidy > 2?
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py-ARD doesn't seem to have a redux mode for first-field DNA nomenclature yet.
The current US organ allocation system supports all three of these HLA specificities: `DRB3*02:02`, `DRB3*02`, and `DR…
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Add a feature that will allow py-ard to expand an allele the list of WHO antigen specificities under the new system https://pubmed.ncbi.nlm.nih.gov/35538616/ .
Based the input of an allele, return…
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hi jiabo，
During genotype processing with `myGAPIT
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Hi. i have provided the two different alleles in my reference sequence. however, i'm not sure if kallisto can handle this properly. also, what happens in the case of homozygosity? is the tpm reported …
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Add HiC-pro functions for allele-specific analysis
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### Description of the bug
I am running a single sample, and ended up assigning the same ID for both "sample" and "case" columns in the input samplesheet.
This crashes in a step where Tomte attemp…