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broadinstitute / gtex-pipeline

GTEx & TOPMed data production and analysis pipelines
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criterion or cut-off used in GTEx v8.signif_variant_gene_pairs.txt #72

Closed Shicheng-Guo closed 3 years ago

Shicheng-Guo commented 3 years ago

I am wondering which criterion or cut-off were used to generate GTEx v8.signif_variant_gene_pairs.txt.gz. I notice some P-values are very large which is closed to 0.0001

Take _Brain_Cortex.v8.signif_variant_genepairs.txt.gz as an example: 

zcat Brain_Cortex.v8.signif_variant_gene_pairs.txt.gz | awk 'NR==1 ||$7>0.0001'  | head

variant_id      gene_id tss_distance    ma_samples      ma_count        maf     pval_nominal    slope   slope_se        pval_nominal_threshold  min_pval_nominal        pval_beta
chr1_591531_G_A_b38     ENSG00000279457.4       396120  4       4       0.0097561       0.000147033     -1.97726        0.508747        0.000155753     2.18013e-05     0.0190512
chr1_26145252_C_A_b38   ENSG00000142675.17      -32151  105     137     0.334146        0.000108614     -0.287931       0.0725949       0.000113439     1.59709e-42     4.5477e-37
chr1_26341905_C_T_b38   ENSG00000142675.17      164502  74      81      0.197561        0.000103826     -0.362586       0.0911469       0.000113439     1.59709e-42     4.5477e-37
chr1_26348428_G_A_b38   ENSG00000142675.17      171025  74      81      0.197561        0.000103826     -0.362586       0.0911469       0.000113439     1.59709e-42     4.5477e-37
chr1_27881801_C_A_b38   ENSG00000117748.9       -32945  126     154     0.37561 0.000111819     0.320871        0.0810554       0.00011394      1.76558e-53     2.79927e-47
chr1_27951627_G_A_b38   ENSG00000158161.15      -137069 141     176     0.429268        0.000109464     0.236155        0.0595714       0.000114127     2.93955e-15     1.58653e-11
chr1_28026143_C_G_b38   ENSG00000158161.15      -62553  124     152     0.370732        0.000104884     -0.244385       0.0614744       0.000114127     2.93955e-15     1.58653e-11
chr1_28042768_G_A_b38   ENSG00000158161.15      -45928  125     153     0.373171        0.000101399     0.245274        0.0615617       0.000114127     2.93955e-15     1.58653e-11
chr1_28064971_T_C_b38   ENSG00000158161.15      -23725  124     152     0.370732        0.000104884     0.244385        0.0614744       0.000114127     2.93955e-15     1.58653e-11
francois-a commented 3 years ago

Hi, please see Section 4.2 in https://www.science.org/doi/suppl/10.1126/science.aaz1776/suppl_file/aaz1776_aguet_sm.pdf for the description of how pval_nominal_threshold was calculated. The code is available here.