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SBIMB / StellarPGx

Calling star alleles in highly polymorphic pharmacogenes (e.g. CYP450 genes) by leveraging genome graph-based variant detection.
MIT License
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StellarPGx treating PCR amplicons as gene copy #26

Closed kiflu-23 closed 1 year ago

kiflu-23 commented 1 year ago

I am running CYP2D6 genotyping using short-read targeted sequencing and ; 1 . I was able to perform variant calling to all my sample but received allele calling only almost half of my samples. I was wondering if there is any particular reason or am I doing something wrong ?

  1. StellarPGx is treating the PCR amplicons as copy number of gene such as "1/1x1546 ". Is there a way to avoid that? Kind regards,

Kiflu

twesigomwedavid commented 1 year ago

@kiflu-23, Thanks. We strongly discourage using StellarPGx for amplicon data at this time. The pipeline currently supports only high-coverage short-read WGS data as input. We are also working on support for long-read data but this is still in the beta phase.

kiflu-23 commented 1 year ago

Hi David,

Thank you for prompt response. About the long-read was also my another question, thank you for answering in advance. And StellarPGx only support bam file not vcf file, right?

Regards,

twesigomwedavid commented 1 year ago

No worries. Yes, it requires the BAM file because the algorithm is currently set up to detect both SNV-defined haplotypes and structural variants.