Bug(incorrect matching of data)

[karlnyr]

We recently discovered a case where the variants were told to be mismatched by the UI which was also confirmed by using the genotype check CLI command.

However, when we investigated these variants further we found that:

• The sample was Homozygous (0 reads supporting REF) for ALT
• The sample was Homozygous for ALT in both MAF and Sequence data
• The positions of concern are on different chromosomes and are not a specific base.

This is very concerning - as it would seem that either the data uploaded to Genotype is not what we believe it to be OR we are doing an incorrect match for these Homozygous calls.

[Vince-janv]

Issue caused by demux using wrong sample sheet, and hence reads from multiple samples (see deviation). Genotype was functioning correctly. Overwrite the previous data using cg upload genotypes <case_id> -f