The documents to be selected look something like this:

{
"_id": {
"$oid": "6272c580d4400d8cb10d5406"
},
"#CHROM": 1,
"POS": 286747,
"ID": "rs369556846",
"REF": "A",
"ALT": "G",
"QUAL": ".",
"FILTER": ".",
"INFO": [{
"RS": 369556846,
"RSPOS": 286747,
"dbSNPBuildID": 138,
"SSR": 0,
"SAO": 0,
"VP": "0x050100000005150026000100",
"WGT": 1,
"VC": "SNV",
"CAF": [{
"$numberDecimal": "0.9381"
}, {
"$numberDecimal": "0.0619"
}],
"COMMON": 1,
"TOPMED": [{
"$numberDecimal": "0.88411856523955147"
}, {
"$numberDecimal": "0.11588143476044852"
}]
},
["SLO", "ASP", "VLD", "G5", "KGPhase3"]
]
}

For a basic annotation (https://en.wikipedia.org/wiki/SNP_annotation) scenario, we need such query:

{'ID': {'$in': ['rs369556846', 'rs2185539', 'rs2519062', 'rs149363311', 'rs55745762', <...>]}}
, where <...> means hundreds/thousands of values.

Such query is executed in a few seconds.

More complex annotation queries:

{'$or': [{'#CHROM': 1, 'POS': 1499125}, {'#CHROM': 1, 'POS': 1680158}, {'#CHROM': 1, 'POS': 1749174}, {'#CHROM': 1, 'POS': 3061224}, {'#CHROM': 1, 'POS': 3589337}, <...>]}

{'$or': [{'ID': 'rs149434212', 'REF': 'C', 'ALT': 'T'}, {'ID': 'rs72901712', 'REF': 'G', 'ALT': 'A'}, {'ID': 'rs145474533', 'REF': 'G', 'ALT': 'C'}, {'ID': 'rs12096573', 'REF': 'G', 'ALT': 'T'}, {'ID': 'rs10909978', 'REF': 'G', 'ALT': 'A'}, <...>]}

Despite the involvement of IXSCAN, they run many hours.

Please test aforementioned queries thoroughly and improve the performance of their execution. This will help science!