Changes between Version 6 and Version 7 of net.sf.basedb.varsearch/using


Ignore:
Timestamp:
Aug 28, 2023, 11:25:05 AM (9 months ago)
Author:
Nicklas Nordborg
Comment:

Clarification about chromosome names

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  • net.sf.basedb.varsearch/using

    v6 v7  
    8484 * `ref:` Reference allele
    8585 * `alt:` Alternate allele
    86  * `chrom:` Name of chromosome(eg. ''chr1'', ''chr2'', etc)
     86 * `chrom:` Name of chromosome (eg. ''chr1'', ''chr2'', ..., ''chr22'', ''chrX'', ''chrY'' and ''chrM'')
    8787 * `pos:` Location within the chromosome. The location is also indexed using the chromsome name as a field name. Thus, the query string `chrom:chr17 AND pos:7675189` can be written as `chr17:7675189` (recommended).
    8888 * `effect:` Expected effect of the variant as determined by !SnpEff. There is a [https://pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details table with a list of possible values]. The `_variant` suffix is ignored for those values that have it.