Wrong scaffold coverage calculation when using coverage file

[adityabandla]

I ran the refinem scaffold_stats & outliers command with a custom coverage file using the --coverage_file option. Some contigs got flagged as having zero coverage across all samples.

However, when I had a look at the coverage file, the contig did have coverage values across several samples. Second, I had a look at the scaffold coverage value in the outliers.tsv file for this contig and it did not correspond with the mean or median for that contig. I am a bit lost as to what is going on here

[donovan-h-parks]

Hi. If you can send me the relevant data via email (donovan.parks [at] gmail.com) I can take a look. Please indicate the exact command you are running and one or more contigs that look problematic.

[adityabandla]

Sent!

[adityabandla]

The issue with zero coverage goes away when the coverage file has column names. However, the calculation of scaffold_coverage in outliers.tsv still seems off

[donovan-h-parks]

Are all the column names unique? This is also a requirement.

[adityabandla]

Yes, the column names are all unique. I am just trying to understand the math behind the column scaffold coverage