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Add checks for genotype file uploads #32

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Cristianetaniguti opened this issue Aug 13, 2024 · 2 comments
Open

Add checks for genotype file uploads #32

Cristianetaniguti opened this issue Aug 13, 2024 · 2 comments
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@Cristianetaniguti
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Cristianetaniguti commented Aug 13, 2024

Confirm that the user uploaded genotype files are valid before starting each analysis

  • Confirm that their are no duplicate sample IDs
    • If there are, list the IDs to the user, and add the option to have them removed from the analysis or to pause the analysis
  • Check that the max ploidy level in the genotypes file agrees with the user selected ploidy level
  • Check if there are multiallelic markers
  • Check if the required field is present. Exemple: GT, AD, DP
@Cristianetaniguti
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VCFs without updog quality measures are returning errors in the VCF Filtering tab.

@Cristianetaniguti
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Currently, each tab has a different way to process the VCF and MADC file, filtering for different aspects. It would be better if we have a single function applied to every tab to check the files format and if they have all information needed. This will reduce code redundancy and avoid bugs while users are uploading files.

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