Uploads of completed analyses results that are stored in Housekeeper happen automatically.
@ rasta:~/servers/crontab/upload-auto.sh
$ cg upload auto
$ cg upload -f FAMILY-ID
This process is split into multiple steps:
Coverage and completeness levels calculated by Sambamba are uploaded to Chanjo. Only one set of results are stored for each sample so old results will automatically replace previous ones.
Coverage/completeness is stored on transcript level for all RefSeq transcripts (+ MT all transcripts) as defined in Scout.
cg upload coverage FAMILY-ID
We deliver variants along with annotations to Scout - the main portal for data delivery.