doc/README_GDS.struct.md

In belleau/aicsPaper: Accurate Inference of Genetic Ancestry from Cancer Sequencing

GDS file structure

The base for 1KG

File: /mnt/wigclust5/data/unsafe/belleau/process1000G/samples1000gUnrelated/data/genoGDS1KG.2022.03.22/matGeno1000g.gds (15.4G)
+    [  ] *
|--+ sample.id   { Str8 2548, 19.9K }
|--+ sample.annot   [ data.frame ] *
|  |--+ sex   { Str8 2548, 5.0K }
|  |--+ pop.group   { Str8 2548, 10.0K }
|  |--+ superPop   { Str8 2548, 10.0K }
|  \--+ batch   { Float64 2548, 19.9K }
|--+ snp.id   { Str8 24542710, 223.5M }
|--+ snp.chromosome   { UInt16 24542710, 46.8M }
|--+ snp.position   { Int32 24542710, 93.6M }
|--+ snp.allele   { Str8 24542710, 93.6M }
|--+ snp.AF   { PackedReal24 24542710, 70.2M }
|--+ snp.EAS_AF   { PackedReal24 24542710, 70.2M }
|--+ snp.EUR_AF   { PackedReal24 24542710, 70.2M }
|--+ snp.AFR_AF   { PackedReal24 24542710, 70.2M }
|--+ snp.AMR_AF   { PackedReal24 24542710, 70.2M }
|--+ snp.SAS_AF   { PackedReal24 24542710, 70.2M }
|--+ genotype   { Bit2 24542710x2548, 14.6G }
\--+ sample.ref   { Bit1 2548, 319B }

If we add the information relative to specific studies we want to infer the ancestry.

File: /mnt/wigclust15/data/unsafe/belleau/TCGA-OV-WXS/data/genoGDS1KG.TCGA-OV.2022.03.30/matGeno1000g.gds (15.5G)
+    [  ] *
|--+ sample.id   { Str8 2558, 20.2K }
|--+ sample.annot   [ data.frame ] *
|  |--+ sex   { Str8 2558, 5.0K }
|  |--+ pop.group   { Str8 2558, 10.2K }
|  |--+ superPop   { Str8 2558, 10.0K }
|  \--+ batch   { Float64 2558, 20.0K }
|--+ snp.id   { Str8 24516859, 223.2M }
|--+ snp.chromosome   { UInt16 24516859, 46.8M }
|--+ snp.position   { Int32 24516859, 93.5M }
|--+ snp.allele   { Str8 24516859, 93.5M }
|--+ snp.AF   { PackedReal24 24516859, 70.1M }
|--+ snp.EAS_AF   { PackedReal24 24516859, 70.1M }
|--+ snp.EUR_AF   { PackedReal24 24516859, 70.1M }
|--+ snp.AFR_AF   { PackedReal24 24516859, 70.1M }
|--+ snp.AMR_AF   { PackedReal24 24516859, 70.1M }
|--+ snp.SAS_AF   { PackedReal24 24516859, 70.1M }
|--+ genotype   { Bit2 24516859x2558, 14.6G }
|--+ sample.ref   { Bit1 2548, 319B }
|--+ study.offset   { Int32 1, 4B }
|--+ study.list   [ data.frame ] *
|  |--+ study.id   { Str8 1, 14B }
|  |--+ study.desc   { Str8 1, 16B }
|  \--+ study.platform   { Str8 1, 4B }
\--+ study.annot   [ data.frame ] *
   |--+ data.id   { Str8 10, 170B }
   |--+ case.id   { Str8 10, 130B }
   |--+ sample.type   { Str8 10, 140B }
   |--+ diagnosis   { Str8 10, 20B }
   |--+ source   { Str8 10, 60B }
   \--+ study.id   { Str8 10, 140B }

The phase GDS for 1KG

It includes the linkage disequilibrium and the gene info for the allelic of the RNA seq (Not show yet)

File: /mnt/wigclust6/data/unsafe/belleau/process1000G/samples1000gUnrelated/data/genoGDS1KG.2022.04.03/matPhase1000g.gds (5.1G)
+    [  ]
\--+ phase   { Bit2 24516859x2548 LZ4_ra(35.0%), 5.1G }

A group of GDS specific to each sample we want to infor

Principaly use for the simulation

File: /mnt/wigclust15/data/unsafe/belleau/TCGA-OV-WXS/data/genoGDS1KG.TCGA-OV.samples/TCGA-25-2404-01A-01W-0799-08.gds (164.1M)
+    [  ]
|--+ Ref.count   { SparseInt16 24516859x1, 7.2M }
|--+ Alt.count   { SparseInt16 24516859x1, 1.0M }
|--+ Total.count   { SparseInt16 24516859x1, 7.6M }
|--+ pruned.study   { Str8 237908, 2.2M }
|--+ sampleStudy   { Str8 1, 29B }
|--+ sample.id   { Str8 2470, 19.3K }
|--+ snp.id   { Str8 237908, 2.2M }
|--+ snp.chromosome   { Int32 237908, 929.3K }
|--+ snp.position   { Int32 237908, 929.3K }
|--+ snp.index   { Int32 237908, 929.3K }
|--+ genotype   { Bit2 237908x2470, 140.1M }
|--+ SamplePos   { Float64 1, 8B }
|--+ lap   { PackedReal8 237908, 232.3K }
\--+ segment   { UInt32 237908, 929.3K }

A GDS phase specific for a study with with a smaller number of SNV

The snp.id are the union the snp.id of GDSSample

File: /mnt/wigclust15/data/unsafe/belleau/TCGA-OV-WXS/data/genoGDS1KG.TCGA-OV.samples/phase1KG.gds (434.6M) + [ ] |--+ snp.id { Str8 722473, 6.6M } |--+ snp.index { Int32 722473, 2.8M } --+ phase { Bit2 722473x2469, 425.3M }

belleau/aicsPaper documentation built on Aug. 4, 2022, 1:12 a.m.