Implement wizard for building database of variant frequencies in SCAN-B samples
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
The annotation/filtering step in the variant calling pipeline is using a database with counts and frequencies for variants that has been found in the SCAN-B data. The current database was built from the release 3 data. It would be nice to have a wizard for building a new database. The input would be an item list with alignments. A script is generated that takes the raw variant calling file together with the patient and counts all variants. For each variant it should count the total number of times it has been seen and the number of patients. Results is saved to a VCF file that is compatible with the existing database.