File formatting¶
PAINTOR¶
Input requirement¶
- Locus file (contain Zscore)
- LD matrix file
- Annotation matrix file
For locus file, first line must be the header, only Zscore is required, other information could also be added.
For LD matrix file, if you have the raw genotype data, you can generate the LD matrix yourself, but if you don't, you can use the 1000 Genome data as the reference and use the script provided by PAINTOR to generate the LD matrix
Note: Snps in the locus file must be in the same order as in the LD matrix file and the annotation matrix file
If finemapping alone¶
| Header | Option | Note |
|---|---|---|
| Zscore | required |
If using 1000G reference to generate LD matrix (most common case)¶
| Header | Option | Note |
|---|---|---|
| chr | required | |
| pos | required | |
| effective allele | required | |
| baseline allele | required | |
| Zscore | required |
fgwas¶
Input requirement¶
- Only one file containing both Zscore and functional annotation
fgwas does NOT require a LD matrix file, but it require the Zscore and the annotations to be incorporated into ONE file. And all loci should be merged into ONE file and identified by a SEGNUMBER column.
In addition, it has different input requirement for quantitative trait and case-control trait
Quantitative trait¶
The columns have no enforced order, but are identified from the header
Type 1¶
| Header | Option | Note |
|---|---|---|
| SNPID | required | |
| CHR | required | |
| POS | required | |
| F | required | allele frequency of one of the alleles of the SNP |
| Z | required | Zscore |
| N | required | sample size |
| SEGNUMBER | required | each locus should have a unique SEGNUMBER, and the file should be ordered accordingly |
| annotation1 | optional | |
| annotation2 | optional | |
| ... |
Type 2¶
| Header | Option | Note |
|---|---|---|
| SNPID | required | |
| CHR | required | |
| POS | required | |
| F | required but not used | allele frequency of one of the alleles of the SNP |
| Z | required | Zscore |
| N | required but not used | sample size |
| SE | required | standard error |
| SEGNUMBER | required | each locus should have a unique SEGNUMBER, and the file should be ordered accordingly |
| annotation1 | optional | |
| annotation2 | optional | |
| ... |
Warning
for type 2, even though input SE will override F and N, you still need to add these two columns otherwise the program will raise an error. If you do not have the real value of F and N, you can add some pseudo values since they will not be used
Case/control studies¶
Type 1¶
| Header | Option | Note |
|---|---|---|
| SNPID | required | |
| CHR | required | |
| POS | required | |
| F | required | allele frequency of one of the alleles of the SNP |
| Z | required | Zscore |
| NCASE | required | number of cases used in the association study at this SNP |
| NCONTROL | required | number of controls used in the association study at this SNP |
| SEGNUMBER | required | each locus should have a unique SEGNUMBER, and the file should be ordered according to this column |
| annotation1 | optional | |
| annotation2 | optional | |
| ... |
Type 2¶
| Header | Option | Note |
|---|---|---|
| SNPID | required | |
| CHR | required | |
| POS | required | |
| F | required but not used | allele frequency of one of the alleles of the SNP |
| Z | required | Zscore |
| NCASE | required but not used | number of cases used in the association study at this SNP |
| NCONTROL | required but not used | number of controls used in the association study at this SNP |
| SE | required | standard error |
| SEGNUMBER | required | each locus should have a unique SEGNUMBER, and the file should be ordered according to this column |
| annotation1 | optional | |
| annotation2 | optional | |
| ... |
Warning
For type 2, even though input SE will override F and NCASE and NCONTROL, you still need to add these two columns otherwise the program will raise an error. If you do not have the real value of F and N, you can add some pseudo values since they will not be used
CAVIAR¶
to be added
CAVIARBF¶
C++ Version¶
Input requirement¶
- Marginal test statistics file (Z-score file)
- Correlation matrix file (LD matrix file)
Example¶
Z-score file¶
This file should NOT contain header
rs11922846 0.41199
rs2587938 -0.631405
rs1351949 0.269231
rs2587940 -0.786003
rs1825507 -0.514003
LD matrix file¶
This file should NOT contain header
1.0000e+00 3.4753e-01 1.0000e+00 3.4492e-01 4.3334e-01
3.4753e-01 1.0000e+00 3.4753e-01 9.8494e-01 -2.3178e-01
1.0000e+00 3.4753e-01 1.0000e+00 3.4492e-01 4.3334e-01
3.4492e-01 9.8494e-01 3.4492e-01 1.0000e+00 -2.3003e-01
4.3334e-01 -2.3178e-01 4.3334e-01 -2.3003e-01 1.0000e+00
R Version¶
R version can incorporate functional annotations into fine-mapping process
Input requirement¶
- Marginal test statistics file (Z-score file)
- Correlation matrix file (LD matrix file)
- Annotation file
Naming of these three files are as follows:
- <z-score-file>
- <z-score-file>.LD
- <z-score-file>.annotations
Example¶
Naming¶
gwas_summary_3_4750808.processed gwas_summary_3_4750808.processed.LD gwas_summary_3_4750808.processed.annotations
Z-score file¶
This file should NOT contain header
rs11922846 0.41199
rs2587938 -0.631405
rs1351949 0.269231
rs2587940 -0.786003
rs1825507 -0.514003
LD matrix file¶
This file should NOT contain header
1.0000e+00 3.4753e-01 1.0000e+00 3.4492e-01 4.3334e-01
3.4753e-01 1.0000e+00 3.4753e-01 9.8494e-01 -2.3178e-01
1.0000e+00 3.4753e-01 1.0000e+00 3.4492e-01 4.3334e-01
3.4492e-01 9.8494e-01 3.4492e-01 1.0000e+00 -2.3003e-01
4.3334e-01 -2.3178e-01 4.3334e-01 -2.3003e-01 1.0000e+00
Annotation file¶
This file should NOT contain header, for CAVIARBF R version, annotations could be binary or continuous value.
This example has 7 annotations
0 0 0 0 0 1 0
0 0 0 0 0 1 0
0 0 0 0 0 1 0
0 1 0 0 0 1 0
0 0 0 0 0 0 0