Namespace(genes='/oak/stanford/groups/akundaje/soumyak/refs/gencode/hg38/hg38.gencode.protein_coding.tss.bed', list='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_summary/asd/trevino_2021/K562_bias/trevino_2021.c4.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/asd/trevino_2021/K562_bias/trevino_2021.c4', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/trevino_2021/peaks/overlap/trevino_2021.c4.overlap.peaks.bed.gz', schema='chrombpnet') Namespace(genes='/oak/stanford/groups/akundaje/soumyak/refs/gencode/hg38/hg38.gencode.protein_coding.tss.bed', list='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_summary/asd/trevino_2021/K562_bias/trevino_2021.c4.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/asd/trevino_2021/K562_bias/trevino_2021.c4', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/trevino_2021/peaks/overlap/trevino_2021.c4.overlap.peaks.bed.gz', schema='chrombpnet') chr pos end allele1 allele2 variant_id 44909 chr1 843979 843980 A G chr1:843980:A:G 1968 chr1 848166 848167 A G chr1:848167:A:G 1969 chr1 894776 894777 A G chr1:894777:A:G 44237 chr1 915678 915679 G A chr1:915679:G:A 1544 chr1 932169 932170 C G chr1:932170:C:G Variants table shape: (84980, 6) annotating with closest genes 0 1 2 3 4 5 6 7 8 9 \ 0 chr1 843979 843980 A G chr1:843980:A:G chr1 923923 923924 SAMD11 1 chr1 843979 843980 A G chr1:843980:A:G chr1 959308 959309 NOC2L 2 chr1 843979 843980 A G chr1:843980:A:G chr1 960584 960585 KLHL17 3 chr1 848166 848167 A G chr1:848167:A:G chr1 923923 923924 SAMD11 4 chr1 848166 848167 A G chr1:848167:A:G chr1 959308 959309 NOC2L 10 11 12 13 14 0 0 + ENSG00000187634.13 protein_coding 79944 1 0 - ENSG00000188976.11 protein_coding 115329 2 0 + ENSG00000187961.15 protein_coding 116605 3 0 + ENSG00000187634.13 protein_coding 75757 4 0 - ENSG00000188976.11 protein_coding 111142 Closest genes table shape: (254940, 15) annotating with peak overlap chr pos end allele1 allele2 variant_id 0 chr1 1201166 1201167 C A chr1:1201167:C:A 1 chr1 1574250 1574251 C A chr1:1574251:C:A 2 chr1 2195639 2195640 C G chr1:2195640:C:G 3 chr1 2278991 2278992 C T chr1:2278992:C:T 4 chr1 2279142 2279143 C G chr1:2279143:C:G Peak overlap table shape: (3507, 6) chr pos allele1 allele2 variant_id logfc.mean \ 0 chr1 3747728 T C chr1:3747728:T:C 0.022437 1 chr1 117942118 T G chr1:117942118:T:G 0.012888 2 chr1 163337297 C A chr1:163337297:C:A -0.073444 3 chr1 32951474 G C chr1:32951474:G:C 0.100043 4 chr1 214496189 G C chr1:214496189:G:C -0.001287 logfc.mean.pval abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.623230 0.022437 0.626760 0.007352 ... 1 0.698625 0.016983 0.700558 0.009212 ... 2 0.281392 0.073444 0.277886 0.020298 ... 3 0.182101 0.100043 0.185009 0.035664 ... 4 0.676846 0.018270 0.676863 0.009802 ... logfc_x_jsd_x_active_allele_quantile.mean.pval \ 0 0.142664 1 0.757371 2 0.367119 3 0.342758 4 0.694804 abs_logfc_x_jsd_x_active_allele_quantile.mean \ 0 9.295310e-05 1 3.489207e-07 2 9.933279e-06 3 1.576590e-05 4 6.063241e-07 abs_logfc_x_jsd_x_active_allele_quantile.mean.pval closest_gene_1 \ 0 0.145252 CCDC27 1 0.758298 WDR3 2 0.364622 RGS5 3 0.345742 RNF19B 4 0.694766 PTPN14 gene_distance_1 closest_gene_2 gene_distance_2 closest_gene_3 \ 0 1267 SMIM1 25022 LRRC47 1 12397 GDAP2 12497 SPAG17 2 15506 NUF2 70720 RGS4 3 13335 TMEM54 50036 HPCA 4 56260 CENPF 106997 SMYD2 gene_distance_3 peak_overlap 0 48770 False 1 243110 False 2 268521 False 3 65479 False 4 215086 False [5 rows x 34 columns] Annotation table shape: (84980, 34) DONE Done Annotating