gnomad-structural-variants-data_description
Bed Example
The bed file was obtained from original source for GRCh37
#chrom start end name svtype ALGORITHMS BOTHSIDES_SUPPORT CHR2 CPX_INTERVALS CPX_TYPE END2 ENDEVIDENCE HIGH_SR_BACKGROUND PCRPLUS_DEPLETED PESR_GT_OVERDISPERSION POS2 PROTEIN_CODING__COPY_GAIN PROTEIN_CODING__DUP_LOF PROTEIN_CODING__DUP_PARTIAL PROTEIN_CODING__INTERGENIC PROTEIN_CODING__INTRONIC PROTEIN_CODING__INV_SPAN PROTEIN_CODING__LOF PROTEIN_CODING__MSV_EXON_OVR PROTEIN_CODING__NEAREST_TSS PROTEIN_CODING__PROMOTER PROTEIN_CODING__UTR SOURCE STRANDS SVLEN SVTYPE UNRESOLVED_TYPE UNSTABLE_AF_PCRPLUS VARIABLE_ACROSS_BATCHES AN AC AF N_BI_GENOS N_HOMREF N_HET N_HOMALT FREQ_HOMREF FREQ_HET FREQ_HOMALT MALE_AN MALE_AC MALE_AF MALE_N_BI_GENOS MALE_N_HOMREF MALE_N_HET MALE_N_HOMALT MALE_FREQ_HOMREF MALE_FREQ_HET MALE_FREQ_HOMALT MALE_N_HEMIREF MALE_N_HEMIALT MALE_FREQ_HEMIREF MALE_FREQ_HEMIALT PAR FEMALE_AN FEMALE_AC FEMALE_AF FEMALE_N_BI_GENOS FEMALE_N_HOMREF FEMALE_N_HET FEMALE_N_HOMALT FEMALE_FREQ_HOMREF FEMALE_FREQ_HET FEMALE_FREQ_HOMALT POPMAX_AF AFR_AN AFR_AC AFR_AF AFR_N_BI_GENOS AFR_N_HOMREF AFR_N_HET AFR_N_HOMALT AFR_FREQ_HOMREF AFR_FREQ_HEAFR_FREQ_HOMALT AFR_MALE_AN AFR_MALE_AC AFR_MALE_AF AFR_MALE_N_BI_GENOS AFR_MALE_N_HOMREF AFR_MALE_N_HET AFR_MALE_N_HOMALT AFR_MALE_FREQ_HOMREF AFR_MALE_FREQ_HET AFR_MALE_FREQ_HOMALT AFR_MALE_N_HEMIREF AFR_MALE_N_HEMIALT AFR_MALE_FREQ_HEMIREF AFR_MALE_FREQ_HEMIALT AFR_FEMALE_AN AFR_FEMALE_AC AFR_FEMALE_AF AFR_FEMALE_N_BI_GENOS AFR_FEMALE_N_HOMREF AFR_FEMALE_N_HET AFR_FEMALE_N_HOMALT AFR_FEMALE_FREQ_HOMREF AFR_FEMALE_FREQ_HET AFR_FEMALE_FREQ_HOMALT AMR_AN AMR_AC AMR_AF AMR_N_BI_GENOS AMR_N_HOMREF AMR_N_HET AMR_N_HOMALT AMR_FREQ_HOMREF AMR_FREQ_HET AMR_FREQ_HOMALT AMR_MALE_AN AMR_MALE_AC AMR_MALE_AF AMR_MALE_N_BI_GENOS AMR_MALE_N_HOMREF AMR_MALE_N_HET AMR_MALE_N_HOMALT AMR_MALE_FREQ_HOMREF AMR_MALE_FREQ_HET AMR_MALE_FREQ_HOMALT AMR_MALE_N_HEMIREF AMR_MALE_N_HEMIALT AMR_MALE_FREQ_HEMIREF AMR_MALE_FREQ_HEMIALT AMR_FEMALE_AN AMR_FEMALE_AC AMR_FEMALE_AF AMR_FEMALE_N_BI_GENOS AMR_FEMALE_N_HOMREF AMR_FEMALE_N_HET AMR_FEMALE_N_HOMALT AMR_FEMALE_FREQ_HOMREF AMR_FEMALE_FREQ_HET AMR_FEMALE_FREQ_HOMALT EAS_AN EAS_AC EAS_AF EAS_N_BI_GENOS EAS_N_HOMREF EAS_N_HET EAS_N_HOMALT EAS_FREQ_HOMREF EAS_FREQ_HET EAS_FREQ_HOMALT EAS_MALE_AN EAS_MALE_AC EAS_MALE_AF EAS_MALE_N_BI_GENOS EAS_MALE_N_HOMREF EAS_MALE_N_HET EAS_MALE_N_HOMALT EAS_MALE_FREQ_HOMREF EAS_MALE_FREQ_HET EAS_MALE_FREQ_HOMALT EAS_MALE_N_HEMIREF EAS_MALE_N_HEMIALT EAS_MALE_FREQ_HEMIREF EAS_MALE_FREQ_HEMIALT EAS_FEMALE_AN EAS_FEMALE_AC EAS_FEMALE_AF EAS_FEMALE_N_BI_GENOS EAS_FEMALE_N_HOMREF EAS_FEMALE_N_HET EAS_FEMALE_N_HOMALT EAS_FEMALE_FREQ_HOMREF EAS_FEMALE_FREQ_HET EAS_FEMALE_FREQ_HOMALT EUR_AN EUR_AC EUR_AF EUR_N_BI_GENOS EUR_N_HOMREF EUR_N_HET EUR_N_HOMALT EUR_FREQ_HOMREF EUR_FREQ_HET EUR_FREQ_HOMALT EUR_MALE_AN EUR_MALE_AC EUR_MALE_AF EUR_MALE_N_BI_GENOS EUR_MALE_N_HOMREF EUR_MALE_N_HET EUR_MALE_N_HOMALT EUR_MALE_FREQ_HOMREF EUR_MALE_FREQ_HET EUR_MALE_FREQ_HOMALT EUR_MALE_N_HEMIREF EUR_MALE_N_HEMIALT EUR_MALE_FREQ_HEMIREF EUR_MALE_FREQ_HEMIALT EUR_FEMALE_AN EUR_FEMALE_AC EUR_FEMALE_AF EUR_FEMALE_N_BI_GENOS EUR_FEMALE_N_HOMREF EUR_FEMALE_N_HET EUR_FEMALE_N_HOMALT EUR_FEMALE_FREQ_HOMREF EUR_FEMALE_FREQ_HET EUR_FEMALE_FREQ_HOMALT OTH_AN OTH_AC OTH_AF OTH_N_BI_GENOS OTH_N_HOMREF OTH_N_HET OTH_N_HOMALT OTH_FREQ_HOMREF OTH_FREQ_HET OTH_FREQ_HOMALT OTH_MALE_AN OTH_MALE_AC OTH_MALE_AF OTH_MALE_N_BI_GENOS OTH_MALE_N_HOMREF OTH_MALE_N_HET OTH_MALE_N_HOMALT OTH_MALE_FREQ_HOMREF OTH_MALE_FREQ_HET OTH_MALE_FREQ_HOMALT OTH_MALE_N_HEMIREF OTH_MALE_N_HEMIALT OTH_MALE_FREQ_HEMIREF OTH_MALE_FREQ_HEMIALT OTH_FEMALE_AN OTH_FEMALE_AC OTH_FEMALE_AF OTH_FEMALE_N_BI_GENOS OTH_FEMALE_N_HOMREF OTH_FEMALE_N_HET OTH_FEMALE_N_HOMALT OTH_FEMALE_FREQ_HOMREF OTH_FEMALE_FREQ_HET OTH_FEMALE_FREQ_HOMALT FILTER
1 10641 10642 gnomAD-SV_v2.1_BND_1_1 BND manta False 15 NA NA 10643 10643 PE,SR False False True 10642 NA NA NA False NA NA NA NA NA NA NA NA NA -1 BND SINGLE_ENDER_-- False False 21366 145 0.006785999983549118 10683 10543 135 5 0.9868950247764587 0.012636899948120117 0.00046803298755548894 10866 69 0.00634999992325902 5433 5366 65 2 0.987667977809906 0.011963900178670883 0.000368120992789045 NA NA NA NA False 10454 76 0.007269999943673615227 5154 70 3 0.9860339760780334 0.013392000459134579 0.0005739430198445916 0.015956999734044075 93972 0.007660999894142151 4699 4629 68 2 0.9851030111312866 0.014471200294792652 0.0004256220126990229 5154 33 0.006403000093996525 2577 2544 33 0 0.9871940016746521 0.012805599719285965 0.0NA NA NA NA 4232 39 0.009216000325977802 2116 2079 35 2 0.9825140237808228 0.01654059998691082 0.0009451800142414868 1910 7 0.003664999967440963 955 949 5 1 0.9937170147895813 0.00523559981957078 0.001047119963914156 950 4 0.004211000166833401 475 472 2 1 0.9936839938163757 0.00421052984893322 0.0021052600350230932 NA NA NA NA 952 3 0.0031510000117123127 476473 3 0 0.9936969876289368 0.006302520167082548 0.0 2296 31 0.013501999899744987 1148 11131 0 0.9729970097541809 0.02700350061058998 0.0 1312 13 0.009909000247716904 656 643 13 0.9801830053329468 0.01981710083782673 0.0 NA NA NA NA 976 18 0.018442999571561813 488470 18 0 0.9631149768829346 0.03688519820570946 0.0 7574 32 0.004224999807775021 3787 37528 2 0.9920780062675476 0.007393720094114542 0.0005281229969114065 3374 17 0.005038999952375889 1681671 15 1 0.9905160069465637 0.008891520090401173 0.000592768017668277 NA NA NA NA 41815 0.003587000072002411 2091 2077 13 1 0.9933050274848938 0.006217120215296745 0.00047823999193497188 3 0.015956999734044075 94 91 3 0 0.968084990978241 0.03191490098834038 0.0 76 0.026316000148653984 38 36 2 0 0.9473680257797241 0.05263160169124603 0.0 NA NA NA NA 112 1 0.008929000236093998 56 55 1 0 0.982142984867096 0.017857100814580917 0.0UNRESOLVED
TSV Example
The tsv was obtained from lifted over dataset created by dbVar for GRCh38
#variant_call_accession variant_call_id variant_call_type experiment_id sample_id sampleset_id assembly chrcontig outer_start start inner_start inner_stop stop outer_stop insertion_length variant_region_acc variant_region_id copy_number description validation zygosity origin phenotype hgvs_name placement_method placement_rank placements_per_assembly remap_alignment remap_best_within_cluster remap_coverage remap_diff_chr remap_failure_code allele_count allele_frequency allele_number
nssv15777856 gnomAD-SV_v2.1_CNV_10_564_alt_1 copy number variation 1 1 GRCh38.p12 10 736806 738184 nsv4039284 10__782746___784124______GRCh37.p13_copy_number_variation 0 Remapped BestAvailable Single First Pass 0 1 AC=21,AFR_AC=10,AMR_AC=9,EAS_AC=0,EUR_AC=2,OTH_AC=0AF=0.038889,AFR_AF=0.044643,AMR_AF=0.03913,EAS_AF=0,EUR_AF=0.023256,OTH_AF=0 AN=540,AFR_AN=224,AMR_AN=230,EAS_AN=0,EUR_AN=86,OTH_AN=0
Structural Variant Type Mapping
The source files represented the structural variants with keys using various naming conventions. In the Nirvana JSON output, these keys will be mapped according to the following.
| Nirvana JSON SV Type Key | GRCh37 Source SV Type Key | GRCh38 Source SV Type Key |
|---|---|---|
| copy_number_variation | copy number variation | |
| deletion | DEL, CN=0 | deletion |
| duplication | DUP | duplication |
| insertion | INS | insertion |
| inversion | INV | inversion |
| mobile_element_insertion | INS:ME | mobile element insertion |
| mobile_element_insertion | INS:ME:ALU | alu insertion |
| mobile_element_insertion | INS:ME:LINE1 | line1 insertion |
| mobile_element_insertion | INS:ME:SVA | sva insertion |
| structural alteration | sequence alteration | |
| complex_structural_alteration | CPX |