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.c18.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/asd/trevino_2021/K562_bias/trevino_2021.c18', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/trevino_2021/peaks/overlap/trevino_2021.c18.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.c18.mean.variant_scores.tsv', out_prefix='/oak/stanford/groups/akundaje/projects/neuro-variants/variant_annotations/asd/trevino_2021/K562_bias/trevino_2021.c18', peaks='/oak/stanford/groups/akundaje/projects/neuro-variants/data/processed/trevino_2021/peaks/overlap/trevino_2021.c18.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 1208669 1208670 G A chr1:1208670:G:A 1 chr1 1574250 1574251 C A chr1:1574251:C:A 2 chr1 1594636 1594637 C G chr1:1594637:C:G 3 chr1 2092138 2092139 C T chr1:2092139:C:T 4 chr1 2230686 2230687 C T chr1:2230687:C:T Peak overlap table shape: (3437, 6) chr pos allele1 allele2 variant_id logfc.mean \ 0 chr1 3747728 T C chr1:3747728:T:C 0.019115 1 chr1 117942118 T G chr1:117942118:T:G 0.011621 2 chr1 163337297 C A chr1:163337297:C:A -0.072310 3 chr1 32951474 G C chr1:32951474:G:C 0.193862 4 chr1 214496189 G C chr1:214496189:G:C -0.006893 logfc.mean.pval abs_logfc.mean abs_logfc.mean.pval jsd.mean ... \ 0 0.610108 0.019115 0.608942 0.009989 ... 1 0.741614 0.011621 0.739576 0.012539 ... 2 0.200270 0.072310 0.198023 0.033044 ... 3 0.030275 0.193862 0.030882 0.049666 ... 4 0.811785 0.008271 0.812547 0.008983 ... logfc_x_jsd_x_active_allele_quantile.mean.pval \ 0 0.260525 1 0.806611 2 0.317607 3 0.194131 4 0.925069 abs_logfc_x_jsd_x_active_allele_quantile.mean \ 0 8.474581e-05 1 2.083431e-06 2 6.146582e-05 3 1.836640e-04 4 3.423791e-07 abs_logfc_x_jsd_x_active_allele_quantile.mean.pval closest_gene_1 \ 0 0.262264 CCDC27 1 0.804165 WDR3 2 0.316228 RGS5 3 0.195930 RNF19B 4 0.926107 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