A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).
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Limited compatibility for some processes with non-hg38/hg19 Genomes #30
This issue reports limitations in the SAMURAI pipeline's compatibility with genome builds other than hg38 and hg19. While the pipeline is functional for these two builds, specific steps encounter issues when processing different genomes.
ASCAT.sc: This step currently does not work with the GRCh38 genome build due to hardcoded dependencies. Need to implement an error message or warning informing users of this limitation.
GISTIC analysis: GISTIC analysis relies on internal files that are specifically designed for hg38 and hg19. Need to implement an error message or warning informing users of this limitation.
SaraPotente
commented
3 days ago
Description of the bug
This issue reports limitations in the SAMURAI pipeline's compatibility with genome builds other than hg38 and hg19. While the pipeline is functional for these two builds, specific steps encounter issues when processing different genomes.
Command used and terminal output
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Relevant files
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System information
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