GWAS finishing effort - 402 missing variants

[yk-tanigawa]

It turned out that the summary statistics generated in array-combined/gwas/current does not match the number of expected lines (1,080,969).

A majority of them have 1,080,566 lines indicating that there are 402 variants missing in the summary statistics.

[yk-tanigawa]

• We checked the summary statistics generated in /oak/stanford/groups/mrivas/users/guhan/sandbox/variants_402
• There was an empty file (white_british/ukb24983_v2_hg19.2401-3562.array-combined.HC976.glm.logistic.hybrid) and that file was deleted.
• For each (GBE_ID, pop) pairs, some of them have multiple results files.

[yk-tanigawa]

• We generated the list of (GBE_ID, pop) pairs that should have summary statistics.
• We focused on the ones with 1,080,566 lines in the results directory and asked whether we have the missing summary statistics for the 402 variants.
• It turned out that 346 (GBE_ID, pop) pairs still do not have the results for 402 variants.
• We performed GWAS on those.

[yk-tanigawa]

The summary statistics computed for 402 variants were succesfully integrated into the main file for 14,244 (pop, GBE_ID).

[yk-tanigawa]

https://github.com/rivas-lab/ukbb-tools/tree/master/04_gwas/extras/202006-GWAS-finish/gwas402

[yk-tanigawa]

white_british / QT_FC1002375 has the missing variants

Run the GWAS: 7_gwas.white_british.QT_FC1002375.sh

Merge the file

bash \
/oak/stanford/groups/mrivas/users/ytanigaw/repos/rivas-lab/ukbb-tools/04_gwas/extras/202006-GWAS-finish/gwas369/4_combine.sh \
/oak/stanford/groups/mrivas/ukbb24983/array-combined/gwas/current/white_british/ukb24983_v2_hg19.QT_FC1002375.array-combined.glm.linear.gz \
/oak/stanford/groups/mrivas/users/ytanigaw/repos/rivas-lab/ukbb-tools/04_gwas/extras/202006-GWAS-finish/gwas402/data/white_british/ukb24983_v2_hg19.QT_FC1002375.one_array.PHENO1.glm.linear