Add checks for genotype file uploads

Breeding-Insight / BIGapp

R Shiny app to perform the bioinformatics pipelines developed within Breeding Insight

https://breedinginsight.org/

Apache License 2.0

2 stars 3 forks source link

Open Cristianetaniguti opened 3 months ago

Cristianetaniguti commented 3 months ago

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 commented 3 months ago

VCFs without updog quality measures are returning errors in the VCF Filtering tab.