Query | GenESysV filters and attributes | GEMINI query | AshkenazimTrio (6,312,781 variants) | 1000 Genomes Project phase3 (2504 samples, 85,211,311 variants) | ||
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GenESysV | GEMINI | GenESysV | GEMINI | |||
Get all novel and detrimental variants | Filters: Limit Variants to dbSNP_ID: excluded, IMPACT: HIGH, FILTER: PASS. | select chrom, start, ref., alt, qual, impact_severity, filter from variants where in_dbsnp = 0 and impact_severity == ‘HIGH’ and filter is Null | 0.73 s/0.21 s | 2 m41.35 s/1.06 s | 33.22 s/0.49 s | 2 m42.80s/0.75 s |
(64)b | (74) | (55) | (20) | |||
Attributes: CHROM, POS, REF, ALT, IMPACT, QUAL, FILTER. | ||||||
Get all rare, loss-of-function variants | Filters: EUR_AF (<): 0.01, Consequence: frameshift_variant, splice_acceptor_variant, splice_donor_variant, start_lost, start_retained_variant, stop_gained, stop_lost. | select chrom, start, ref., alt, qual, gene from variants where is_lof = 1 and aaf_1kg_eur < 0.01 and filter is Null limit 400 | 1.20s/0.34 s | 2.39 s/0.35 s | 9.97 s/0.53 s | 2.60s/0.59 s |
(315) | (269) | (400)c | (400)c | |||
FILTER: PASS. | ||||||
Attributes: CHROM, POS, REF, ALT SYMBOL. | ||||||
Get rare, loss-of-function variants and is also heterozygous in selected samples | Filters: Consequence: frameshift_variant, splice_acceptor_variant, splice_donor_variant, start_lost, start_retained_variant, stop_gained, stop_lost. | select chrom, start, ref., alt, qual, gene, gts.HG003, gts.HG004 from variants where is_lof = 1 and aaf_1kg_eur < 0.01 and filter is Null" --gt-filter “gt_types.HG003 == HET” or “gt_types.HG004 == HET” | 0.71 s/0.37 s | 3.21 s/0.47 s | 51.47 s/2.28 s | 1 m33.57 s/3.52 s |
(239)e | (213) | (31) | (36) | |||
FILTER: PASS, EUR_AF (<): 0.01, Sample_ID: HG003d, HG004, GT: 0|1,1|0. | ||||||
Attributes: CHROM, POS, REF, ALT, SYMBOL, Sample_ID, GT. | ||||||
Get missense variants in human HLA region | Filters: CHROM: 6, POS (>=): 28477797, POS (<=): 33448354, Consequence: missense_variant. | Select chrom, start, ref., alt, gene, max_aaf_all, impact, rs_ids from variants where chrom = ‘chr6’ and start > = 28,477,797 and end <= 33,448,354 and impact= ‘missense_variant’ limit 400. | 0.41 s/0.39 s | 3.70s/0.51 s | 6.77 s/0.62 s | 7.72 s/0.78 s |
(400)c | (400)c | (400)c | (400)c | |||
Attributes: CHROM, POS, dbSNP_ID, REF, ALT SYMBOL, MAX_AF. |