|Version 3 (modified by 3 years ago) ( diff ),
How to use the Variant Search extension
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.
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.
The variant database uses Apache Lucene instead of PostgreSQL. Thus, the search field for this column behaves differently from other search fields in BASE.
It is possible to search for raw bioassays that have been indexed or not and the number of variants:
%: Find all indexed raw bioassays
=: Find all raw bioassays that are not indexed
=0: Find indexed raw bioassays with 0 variants
>=500: Find indexed raw bioassays with at least 500 variants
Note! This syntax is similar to the regular BASE syntax, but is for example, not possible to use a list of values:
=1|2 (will not work)
Searching for variants
A typical search in a Lucene database consists of a field name and query string separated by a colon (:). Here are a few examples:
gene:TP53: Find variants in the TP53 gene
chr17:7675189: Find variants at the specified genomic location
c:423C>G: Find variants at the given transcript position
p:C141W: Find variants causing the specified protein change
cosmic:COSV52706449: Find variants for the COSMIC ID
rsid:rs1057519977: Find variants for the dbSNP ID
gt:1/1: Find variants that are homozygous
dp:>=100: Find variants that has been sequenced to a depth 100 or more
vd:>=100: Find variants where at least 100 alternate alleles have been found
af:>0.8: Find variants where the alternate allele frequency is larger than 0.8
effect:synonymous: Find variants where the predicted effect is synonymous
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. Here are the same examples as above:
TP53: Since gene: is the default field
423C>G: Numbers followed by [ACGT] and >
C141W: Single-letter with numbers in-between
COSV52706449: 'COSV' follwed by numbers
rs1057519977: 'rs' followed by numbers
1/1: 0 or 1 with forward slash in-between
Note! If a query don't return the expected result always try again with explicit field prefixes. The following fields are never auto-detected:
It is possible to specify multiple conditions with AND and OR.
TP53 AND 423C>G
TP53 AND (423C>G OR 742C>T)
The AND and OR keywords are case-sensitive and OR is implicit if not specified. Thus, the query string
TP53 and 423C>G will not return the expected results since it is interpreted as:
gene:TP53 OR gene:and OR c:423C>G.
For more information about Lucene query syntax see https://lucene.apache.org/core/8_8_0/queryparser/org/apache/lucene/queryparser/classic/package-summary.html#package.description
The variant database currently contains the following indexed fields:
gene:Gene name from the ncbiRefSeq annotation the SnpEff Gene_Name column. Case-insensitive.
type:Type of variant. Can be one of SNV, Insertion, Deletion, Complex.
cosmic:ID of the variant in the COSMIC database.
rsid:ID of variant in the dbSNP database.
c:Transcript change. Taken from the cosmic_CDS annotation and SnpEff HGVS.c column.
p:Expected amino-acid change in the protein. Taken from cosmic_AA annotation and SnpEff HGVS.p column. Note! COSMIC uses single-letter notation for amino acids, while SnpEff uses three-letter notation. To make things simple, all values have been converted to single-letter notation in the index. See https://www.hgvs.org/mutnomen/codon.html for a table with translations.
chrom:Name of chromosome(eg. chr1, chr2, etc)
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:7675189can be written as
effect:Expected effect of the variant as determined by SnpEff. There is a table with a list of possible values. The
_variantsuffix is ignored for those values that have it.
gt:: Genotype of the variant. Can be one of
dp:: Depth at the variant location.
vd:: Depth of the alternate allele at the variant location.
af:: Allele frequency of the alternate allele.
The query against the Lucene database has a default timeout of 30 seconds. If complete results and information about the variants can't be loaded in that timeout the query will stop and only the results that have been gathered so far are used when matching against raw bioassays. A message is displayed in the column header:
The query did not finish within 30 seconds. Showing results based on 4.3M hits out of 56.1M total hits.
It is possible to change the timeout by appending
/TT to the query string, where
TT is the desired timeout. For example:
chr1/120 will increase the timeout to 120 seconds when searching for all variants in chromosome 1. The timeout is not allowed to be longer than 600 seconds.