susie by tad give snps that are not in tad region.
hsun3163 opened this issue · comments
As demo below, the snps that are used to fine map are not in the "fine map region"
hs3163@node49:/mnt/vast/hpc/csg/molecular_phenotype_calling/eqtl/output/susie_per_gene_tad_2/cache$ zcat demo.ENSG00000001630.unisusie.fit.dlpfc_eqtl.variant.tsv.gz | head
variants snps_index chromosome position ref alt cs_order cs_id log10_base_factor pip z posterior_mean posterior_sd molecular_trait_id finemapped_region_start finemapped_region_end
chr7:89480181_C_T 1 7 89480181 C T 0 None -1.21611029672573;0;0;0;0;0;0;0;0;0 4.829470157119431e-14 1.2370190479200822 -1.2217395717752236e-17 1.1744313146481363e-8 ENSG00000001630 90480000 92480000
chr7:89480347_G_A 2 7 89480347 G A 0 None -0.468029054661293;0;0;0;0;0;0;0;0;0 1.0191847366058937e-13 -1.721307676595514 2.0244642854030178e-15 2.142206834646746e-8 ENSG00000001630 90480000 92480000
chr7:89480582_G_A 3 7 89480582 G A 0 None -1.34371371517411;0;0;0;0;0;0;0;0;0 4.241051954068098e-14 1.1341626290836182 -5.947152839049453e-15 1.046448415490946e-8 ENSG00000001630 90480000 92480000
chr7:89481823_T_TCAAA 4 7 89481823 T TCAAA 0 None -1.67900970197013;0;0;0;0;0;0;0;0;0 3.042011087472929e-14 0.8038294895099635 1.6340102360238463e-15 7.479916733025619e-9 ENSG00000001630 90480000 92480000
chr7:89482247_T_C 5 7 89482247 T C 0 None -1.89967503365067;0;0;0;0;0;0;0;0;0 2.4313884239290928e-14 -0.47471801264963537 8.284991593949965e-16 5.750490562736583e-9 ENSG00000001630 90480000 92480000
chr7:89482999_G_A 6 7 89482999 G A 0 None -1.73072725479902;0;0;0;0;0;0;0;0;0 2.886579864025407e-14 0.7399217431997888 -3.9249960300963515e-16 7.0607311025594075e-9 ENSG00000001630 90480000 92480000
chr7:89483043_T_TG 7 7 89483043 T TG 0 None -1.29970154907714;0;0;0;0;0;0;0;0;0 4.440892098500626e-14 -1.1706537800702028 7.242339111647705e-16 1.0895951285102613e-8 ENSG00000001630 90480000 92480000
chr7:89483179_T_C 8 7 89483179 T C 0 None -1.89487763436464;0;0;0;0;0;0;0;0;0 2.4424906541753444e-14 0.48425283864099006 -1.7623832926305236e-15 5.7866212786035995e-9 ENSG00000001630 90480000 92480000
chr7:89483494_A_G 9 7 89483494 A G 0 None -1.97965592875799;0;0;0;0;0;0;0;0;0 2.2426505097428162e-14 -0.2700865336209036 4.0230626768388057e-16 5.15532512827786e-9 ENSG00000001630 90480000 92480000
This is due to
hs3163@node49:/mnt/vast/hpc/csg/molecular_phenotype_calling/eqtl$ cat /mnt/vast/hpc/csg/molecular_phenotype_calling/eqtl/output/dlpfc_tad_region_list_plink_fi
les/ROSMAP_NIA_WGS.leftnorm.filtered.filtered.tad683.log
PLINK v2.00a2.3LM AVX2 Intel (24 Jan 2020)
Options in effect:
--allow-no-sex
--bfile /mnt/vast/hpc/csg/molecular_phenotype_calling/genotype/ROSMAP_NIA_WGS.leftnorm.filtered.filtered
--chr chr7
--from-bp 89480000
--make-bed
--out /mnt/vast/hpc/csg/molecular_phenotype_calling/eqtl/output/dlpfc_tad_region_list_plink_files/ROSMAP_NIA_WGS.leftnorm.filtered.filtered.tad683
--output-chr chrMT
--to-bp 93480000
Hostname: node42
Working directory: /mnt/vast/hpc/csg/molecular_phenotype_calling/eqtl
Start time: Thu Oct 20 12:27:37 2022
The reason this error occurs is due to fail to set windows == 0 while setting TAD by genes.
Rerunning with the new commands