List Marker Qualifiers
The Solr indexing can be customized to include or exclude only selected qualifiers. Listing all qualifiers stored in the database may help you with your decision on which qualifiers to include or exclude. To list marker qualifiers, run:
PS> list marker_qualifier
┌───────────────────────────────────────────┐
│ [##] QUALIFIER #ENTRIES │
├───────────────────────────────────────────┤
│ [0] AA_# 278,389 │
│ [1] AF_ESP 151,238 │
│ [2] AF_EXAC 253,131 │
│ [3] AF_TGP 177,005 │
│ [4] ALLELEID 784,691 │
│ [5] Alignment end on query 18 │
│ [6] Alignment length 18 │
│ [7] Alignment start on query 18 │
│ [8] BB_# 278,389 │
...
│ [47] Variant_seq 1,090,836 │
│ [48] alleles 3,111,022 │
│ [49] coverage 5,045 │
│ [50] evalue 18 │
│ [51] identity 5,045 │
│ [52] indels 5,045 │
│ [53] matches 5,045 │
│ [54] mismatches 5,045 │
│ [55] reference_peptide 55,234 │
│ [56] unknowns 5,045 │
│ [57] variant_peptide 55,234 │
└───────────────────────────────────────────┘
Type the line [number] to find map sets that use the selected qualifier (ENTER to skip):
If you are interested in listing map sets where a particular qualifier is used, type the corresponding line number:
Type the line [number] to find map sets that use the selected qualifier (ENTER to skip): 18
Marker qualifier Category:
┌──────────────────────────────────────────────────┐
│ MAP_SET_ID ACCESSION #MAPPINGS EXAMPLE │
├──────────────────────────────────────────────────┤
│ 21 IWGSCv1.0 278,113 CRBT │
│ 24 CS_Renan_Genetic 83,721 CRBT │
│ 25 RH_MAPS 8,508 CRBT │
│ 195 IWGSCv2.1 248,688 CRBT │
└──────────────────────────────────────────────────┘
The example values shown on the right represent the shortest possible values. To list all unique qualifier values use the MAP_SET_ID with the command:
Marker qualifiers with example values for map set:/Homo sapiens/GRCh38
┌─────────────────────────────────────────────────────────────────────────────────────────┐
│ [##] QUAL_NAME #ENTRIES EXAMPLE │
├─────────────────────────────────────────────────────────────────────────────────────────┤
│ [0] AF_ESP 94,879 0.00008 │
│ [1] AF_EXAC 165,956 0.00000 │
│ [2] AF_TGP 110,416 0.00000 │
│ [3] ALLELEID 441,959 100000 │
│ [4] CLNDISDB 441,506 . │
│ [5] CLNDISDBINCL 1,104 . │
│ [6] CLNDN 441,506 17-Beta-Hydroxysteroid_Dehydrogenase_III_Deficiency │
│ [7] CLNDNINCL 1,104 2-aminoadipic_2-oxoadipic_aciduria │
│ [8] CLNHGVS 441,959 NC_000001.11:g.100007096A>C │
│ [9] CLNREVSTAT 441,959 criteria_provided,_conflicting_interpretations │
│ [10] CLNSIG 441,506 Affects │
│ [11] CLNSIGCONF 40,857 Benign(1) │
│ [12] CLNSIGINCL 1,104 101229:Pathogenic │
│ [13] CLNVC 441,959 Deletion │
│ [14] CLNVCSO 441,959 SO:0000159 │
│ [15] CLNVI 156,293 ACBD5_@_LOVD:ACBD5_00001|OMIM_Allelic_Variant:616618.0001 │
│ [16] CutFrom 58,684 1 │
│ [17] CutPos 58,684 100000001 │
│ [18] DBVARID 126 nsv1067832 │
│ [19] GENEINFO 441,818 A2M:2|KLRG1:10219 │
│ [20] ID 441,959 10 │
│ [21] MC 440,537 SO:0001574|splice_acceptor_variant │
│ [22] ORIGIN 436,404 0 │
│ [23] RS 441,061 10000 │
│ [24] alleles 708,006 A/C │
└─────────────────────────────────────────────────────────────────────────────────────────┘
Type the line [number] to print all values for selected qualifier (ENTER to skip): 13
Marker qualifier CLNVC:
single_nucleotide_variant
Duplication
Indel
Deletion
Insertion
Inversion
copy_number_loss
Variation
Microsatellite
copy_number_gain
total:441,959 values (distinct:10)
Now you should have more information that will help you decide whether a qualifier is worth to be indexed for search or not.