Changes between Version 1 and Version 2 of net.sf.basedb.varsearch/using

Mar 19, 2021, 11:13:54 AM (3 years ago)
Nicklas Nordborg

Added information about additional indexed fields


  • net.sf.basedb.varsearch/using

    v1 v2  
    3232 * `cosmic:COSV52706449`: Find variants for the COSMIC ID
    3333 * `rsid:rs1057519977`: Find variants for the dbSNP ID
     34 * `gt:1/1`: Find variants that are homozygous
     35 * `dp:>=100`: Find variants that has been sequenced to a depth 100 or more
     36 * `vd:>=100`: Find variants where at least 100 alternate alleles have been found
     37 * `af:>0.8`: Find variants where the alternate allele frequency is larger than 0.8
     38 * `effect:synonymous`: Find variants where the predicted effect is synonymous
    3540**Tip! ** The prefix can in many cases be skipped since it is almost always possible to automatically make an educated guess about the field with some pattern matching on the query string. The **gene:** field is the default and will be used if a field can't be automatically guessed.
    4146 * `COSV52706449`: 'COSV' follwed by numbers
    4247 * `rs1057519977`: 'rs' followed by numbers
     48 * `1/1`: 0 or 1 with forward slash in-between
    4450**Note! ** If a query don't return the expected result always try again
    45 with explicit field prefixes.
     51with explicit field prefixes. The following fields are **never** auto-detected:
     53 * `dp`
     54 * `vd`
     55 * `af`
     56 * `effect`
    4758It is possible to specify multiple conditions with **AND** and **OR**.
    6879 * `chrom:` Name of chromosome(eg. ''chr1'', ''chr2'', etc)
    6980 * `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).
     81 * `effect:` Expected effect of the variant as determined by !SnpEff. There is a [ table with a list of possible values]. The `_variant` suffix is ignored for those values that have it.
     82 * `gt:`: Genotype of the variant. Can be one of `0/1`, `1/0` or `1/1`.
     83 * `dp:`: Depth at the variant location.
     84 * `vd:`: Depth of the alternate allele at the variant location.
     85 * `af:`: Allele frequency of the alternate allele.