# Are there example SAIGE pipelines?

From within Sandbox:

* `/finngen/shared/saige_gwas/20200407_090747/files/saige_pipeline`
* /finngen/shared/r6\_saige/20201006\_141639/files/saige\_pipeline\_R6/wdl/saige\_pipeline\_ps.wdl

For R6:

* [FinnGen SAIGE mixed model association analysis pipeline tools](https://hub.docker.com/r/finngen/saige/tags) (Docker).
* [FinnGen SAIGE pipelines](https://github.com/FINNGEN/saige-pipelines) (GitHub).

For R7 example of saige.json

* saige\_pipeline\_ps\_R7\_input.json

```
{
    "saige_pipeline_ps.docker": "eu.gcr.io/finngen-sandbox-v3-containers/saige:0.36.3.2.finngen.counts.2",
    "saige_pipeline_ps.list_bgen": "LIBRARY_SHARED/r7_bgen_file_list/20210805_071330/files/saige_pipeline/R7_bgen_filelist.txt",
    "saige_pipeline_ps.phenolistfile": "LIBRARY_SHARED/saige_gwas/20200407_090747/files/saige_pipeline/input_data/phenolist.txt",
    "saige_pipeline_ps.loco": "FALSE",
    "saige_pipeline_ps.traitType": "binary",

    "saige_pipeline_ps.null.bedfile": "LIBRARY_RED/finngen_R7/grm_1.0/data/finngen_R7_grm_v1_ld_0.1.bed",
    "saige_pipeline_ps.null.phenofile": "LIBRARY_RED/finngen_R7/phenotype_4.0/data/finngen_R7_cov_pheno_1.0.txt.gz",
    "saige_pipeline_ps.null.covariates":"SEX_IMPUTED,AGE_AT_DEATH_OR_END_OF_FOLLOWUP,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,IS_FINNGEN2_CHIP,BATCH_DS1_BOTNIA_Dgi_norm,BATCH_DS10_FINRISK_Palotie_norm,BATCH_DS11_FINRISK_PredictCVD_COROGENE_Tarto_norm,BATCH_DS12_FINRISK_Summit_norm,BATCH_DS13_FINRISK_Bf_norm,BATCH_DS14_GENERISK_norm,BATCH_DS15_H2000_Broad_norm,BATCH_DS16_H2000_Fimm_norm,BATCH_DS17_H2000_Genmets_norm,BATCH_DS18_MIGRAINE_1_norm,BATCH_DS19_MIGRAINE_2_norm,BATCH_DS2_BOTNIA_T2dgo_norm,BATCH_DS20_SUPER_1_norm,BATCH_DS21_SUPER_2_norm,BATCH_DS22_TWINS_1_norm,BATCH_DS23_TWINS_2_norm,BATCH_DS24_SUPER_3_norm,BATCH_DS25_BOTNIA_Regeneron_norm,BATCH_DS3_COROGENE_Sanger_norm,BATCH_DS4_FINRISK_Corogene_norm,BATCH_DS5_FINRISK_Engage_norm,BATCH_DS6_FINRISK_FR02_Broad_norm,BATCH_DS7_FINRISK_FR12_norm,BATCH_DS8_FINRISK_Finpcga_norm,BATCH_DS9_FINRISK_Mrpred_norm",
    "saige_pipeline_ps.null.sampleID": "FINNGENID",
    "saige_pipeline_ps.null.traceCVcutoff": 0.0025,
    "saige_pipeline_ps.null.ratioCVcutoff": 0.001,
    "saige_pipeline_ps.null.cpu": 32,
    "saige_pipeline_ps.null.mem": 7,
    "saige_pipeline_ps.null.minCovariateCount": 10,

     "saige_pipeline_ps.test.samplefile": "LIBRARY_SHARED/finngen_r7_sample_list/20210805_074404/files/saige_pipeline/finngen_r7_sample_list.txt",
     "saige_pipeline_ps.test.minmac": 5,
     "saige_pipeline_ps.test.analysisType": "additive",

     "saige_pipeline_ps.combine.blacklist": "LIBRARY_SHARED/saige_gwas/20200407_090747/files/saige_pipeline/input_data/nullfile.txt",
     "saige_pipeline_ps.combine.info_threshold": 0.6,
     "saige_pipeline_ps.combine.cpu": 1,
     "saige_pipeline_ps.combine.mem": 7,
     "saige_pipeline_ps.combine.chrcol": "#chrom",
     "saige_pipeline_ps.combine.p_valcol": "pval",
     "saige_pipeline_ps.combine.bp_col": "pos",
     "saige_pipeline_ps.combine.loglog_pval": 10
}
```

.wdl and .json files can be used as input folders in [FinnGen Sandbox Pipeline tool](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/pipelines-tool-instructions/how-to-use-the-pipelines-area)