Changes between Version 2 and Version 3 of net.sf.basedb.varsearch/install


Ignore:
Timestamp:
Dec 21, 2021, 8:44:53 AM (5 months ago)
Author:
Nicklas Nordborg
Comment:

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  • net.sf.basedb.varsearch/install

    v2 v3  
    2121 * The raw bioassay must have a VCF file linked via the '''VCF file type'''. This VCF is assumed to be the filtered VCF file.
    2222 * The raw bioassay may also have a VCF linked via an any-to-any link named '''variants-annotated.vcf.gz'''. This VCF is assumed to be the unfiltered (raw) VCF.
     23 * The raw bioassay may also have more VCF files linked via any-to-any links with names that start with `genotype_`. These VCF files are assumed to be the results of targeted genotyping.
    2324
    24 Indexing is controlled via Item lists. The installation procedure created two item lists:
     25Indexing is controlled via Item lists. The installation procedure created three item lists:
    2526
    2627 * Variant index (filtered)
    2728 * Variant index (all)
     29 * Variant index (targeted genotyping)
    2830
    29 To index the VCF file we need to add raw bioassays to the item lists. Raw bioassays that are added to the ''Variant index (filtered)'' list will get the filtered VCF indexed, and raw bioassays that are added to the ''Variant index (all)'' list will get the full VCF indexed. Usually the indexing will start automatically once the Index Manager detects that there are things to index, but it may take 10-15 minutes. The raw bioassays are removed from the lists after they have been indexed.
     31To index the VCF files we need to add raw bioassays to the item lists. Raw bioassays that are added to the ''Variant index (filtered)'' list will get the filtered VCF indexed, raw bioassays that are added to the ''Variant index (all)'' list will get the full VCF indexed, and raw bioassays that are added to the ''Variant index (targeted genotyping)'' will get the targeted genotyping VCF files indexed. Usually the indexing will start automatically once the Index Manager detects that there are things to index, but it may take 10-15 minutes. The raw bioassays are removed from the lists after they have been indexed.
    3032
    3133== The Index Manager ==