umi stat

[dauss75]

Hello,

I was reviewing data in work/qc/umi/_umi_stats.yaml and /work/align/sample/.family_size_histogram.tsv, and they look quite different. Could you kindly let me know how the metrics in ~_umi_stats.yaml are generated?

Thanks,
Segun

[gabeng]

Hi,

if I am not mistaken, the family_size_historgram.tsv is generated by fgbio and should contain information like this:
http://fulcrumgenomics.github.io/fgbio/metrics/latest/#familysizemetric

The umi_stats.yaml is generated by some bcbio code here:
https://github.com/bcbio/bcbio-nextgen/blob/master/bcbio/qc/umi.py

hth

Ben