Data description
File naming pattern and file structure
Summary association statistics
GWAS summary statistics (tab-delimited, bgzipped, genome build 38, tabix index files included) are named as {endpoint}.gz
. For example, endpoint I9_CHD
has I9_CHD.gz
and I9_CHD.gz.tbi
. Note that the results are based on imputed genotype data and produced using SAIGE and that is why the data is not presented as integers but might contain digits.
To learn more about the methods used, see section GWAS.
The {endpoint}.gz
have the following structure:
*)Note that the results are based on imputed genotype dosages and produced using SAIGE and that is why the data is not presented as integers but might contain digits.
Fine-mapping results
Two fine-mapping methods were used:
Fine-mapping results are tab-delimited and bgzipped.
SuSiE results have the following filename pattern:
{endpoint}.SUSIE.cred.bgz
{endpoint}.SUSIE.snp.bgz
FINEMAP results have the following filename pattern:
{endpoint}.FINEMAP.region.bgz
{endpoint}.FINEMAP.snp.bgz
{endpoint}.FINEMAP.config.bgz
To learn more about the methods used, see section Fine-mapping.
SuSiE output files {endpoint}.SUSIE.snp.bgz
have the following structure:
LD estimation
Linkage disequilibrium (LD) was estimated from SISU v3 for each chromosome. Use the tool LDstore (v1.1) for further usage of the bcor files.
ldstore --bcor FG_LD_chr1.bcor --incl-range 20000000-50000000 --table output_file_name.table
To learn more about the methods used, see section LD estimation.
Variant annotation
The variant annotation has measures (HWE
, INFO
, ...) listed per batch.
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