gnomad-genetics-mcp-server: get variant cooccurrence
gnomad_get_variant_cooccurrenceEstimate whether two variants in the same gene sit on different haplotypes (in trans — compound heterozygous) or on the same one (in cis), from gnomAD v2.1 exome genotypes: the probability of compound heterozygosity and the genotype and haplotype counts behind it, overall and per genetic-ancestry group. For a proband with two rare heterozygous variants in a recessive gene and no parental samples. Takes exactly two GRCh37 chrom-pos-ref-alt IDs and always reads gnomad_r2_1, the only dataset gnomAD serves co-occurrence for, echoing it with GRCh37. A GRCh38 ID can name a different GRCh37 variant or none, so convert GRCh38 IDs first: gnomad_get_variant on dataset gnomad_r2_1 lists their GRCh37 IDs as candidates only when the ID fails there as variant_not_found_other_build; an ID gnomad_r2_1 finds returns a different variant. gnomAD answers only for two different coding or UTR variants of one gene, both in its exome samples with exome allele frequency of 5% or less; any other pair fails as cooccurrence_unavailable with gnomAD's reason. Each count key names variant_ids[0]'s genotype or allele first and variant_ids[1]'s second, and variant_ids can list the pair in another order than sent. The notice carries gnomAD's calibration caveat and its browser's reading of the probability. gnomAD's browser also notes when the pair is found in phase as a multi-nucleotide variant; this tool does not check for one. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/
Tool call template
Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.
{
"id": 1,
"jsonrpc": "2.0",
"method": "tools/call",
"params": {
"arguments": {
"variants": "<variants>"
},
"name": "gnomad_get_variant_cooccurrence"
}
}Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| variants | Yes | The two variants to phase, as GRCh37 chrom-pos-ref-alt IDs. Order does not matter: variant_ids in the output gives the order the counts use. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| error | No | Present when the call failed. Absent on success. | |
| notice | No | gnomAD's calibration caveat and its browser's reading of the probability for this pair. When no sample carries both variants, it adds that the counts come from each variant's separate data and do not account for samples not covered at both sites; that coverage sentence appears only then. | |
| dataset | No | Dataset the counts come from — always gnomad_r2_1, the only one gnomAD serves co-occurrence for. | |
| populations | No | The same counts per genetic-ancestry group, in gnomAD's order. | |
| variant_ids | No | The pair in gnomAD's order, which labels every count: variant_ids[0] is the first token of each key, variant_ids[1] the second. Can differ from the order sent. | |
| genotype_counts | No | Samples per genotype pair. Each key names variant_ids[0]'s genotype first and variant_ids[1]'s second: ref (homozygous reference), het (heterozygous), hom (homozygous alternate). | |
| haplotype_counts | No | gnomAD's estimated haplotype counts, fractional where samples heterozygous for both variants leave the phase to its EM estimate. Each key names variant_ids[0]'s allele first and variant_ids[1]'s second. | |
| reference_genome | No | Reference build of variant_ids — always GRCh37. | |
| p_compound_heterozygous | No | Estimated probability that the two variants lie on different haplotypes (in trans, compound heterozygous). Null when gnomAD computes none, as when either variant has no carrier among these samples — never read null as 0. |