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
.
To learn more about the methods used, see section GWAS.
The {endpoint}.gz
have the following structure:
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.cred_99.bgz
{endpoint}.SUSIE.snp.bgz
FINEMAP results have the following filename pattern:
{endpoint}.FINEMAP.config.bgz
{endpoint}.FINEMAP.region.bgz
{endpoint}.FINEMAP.snp.bgz
To learn more about the methods used, see section Fine-mapping.
{endpoint}.SUSIE.cred.bgz
contain credible set summaries from SuSiE fine-mapping for all genome-wide significant regions. {endpoint}.SUSIE.cred_99.bgz
contain the 99% credible set summaries while the default is 95%. They have the following structure:
{endpoint}.SUSIE.snp.bgz
contain variant summaries with credible set information and have the following structure:
{endpoint}.FINEMAP.config.bgz
contain summary fine-mapping variant configurations from FINEMAP method and have the following structure:
{endpoint}.FINEMAP.region.bgz
contain summary statistics on number of independent signals in each region and have the following structure:
{endpoint}.FINEMAP.snp.bgz
has summary statistics of variants and into what credible set they may belong to. Columns:
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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