Changes between Version 4 and Version 5 of net.sf.basedb.varsearch/using


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Timestamp:
Dec 21, 2021, 9:12:46 AM (3 years ago)
Author:
Nicklas Nordborg
Comment:

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  • net.sf.basedb.varsearch/using

    v4 v5  
    22
    33== Introduction ==
    4 The current search functionality is integrated directly in BASE. Go to the raw bioassays list page and add the **Variant (filtered)** column to the table using the **Columns...** dialog, or right-click on the title row and enabled it from the popup menu.
     4The current search functionality is integrated directly in BASE. Go to the raw bioassays list page and add the **Variant (filtered)**, **Variants (all)** and/or **Variants (targeted)** columns to the table using the **Columns...** dialog, or right-click on the title row and enable them from the popup menu.
    55
    6 By default, the column displays **Yes** or **No** depending on if the VCF file has been indexed or not. If **Yes**, the number of variants is also displayed.
     6By default, the columns display **Yes** or **No** depending on if the VCF file has been indexed or not. If **Yes**, the number of variants is also displayed.
     7
     8 * **Variants (all)**: This index contain all variants found in the variant calling pipeline. There are typically several thousands for each rawbioassay.
     9 * **Variants (filtered)**: This index contain the variants that survived the filtering step in the variant calling pipeline. There are typically less than 100 variants for each raw bioassay.
     10 * **Variants (targeted)**: This index contain the results from the targeted genotyping and include results for both when a variant is found and when it is not found. There are currently 3 sets of targeted genotyping:
     11  - ESR1 (13 resistance mutations related to standard hormone therapy)
     12  - PIK3CA (11 variants related to Alpelisib treatment)
     13  - DPYD (6 variants related to fluoropyrimidine-associated toxicity)
    714
    815== Searching ==
    … …  
    8592 * `af:`: Allele frequency of the alternate allele.
    8693
     94== Notes about the targeted genotyping variants ==
     95
     96The targeted genotyping index behaves a bit differently than the other indexes since it also contain information where the genotype is `0/0`. When searching this index, the default is to automatically exclude entries where the genotype is `0/0`. Otherwise, for example, a search for a gene would return results for all raw bioassays.
     97
     98The exception is when the query string is searching on fields that are related to the genotype: `gt`, `dp`, `vd` and `af`. In this case the `0/0` entries are not excluded.
     99
     100
    87101== Timeouts ==
    88102