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Updated documentation for new trident release #79

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Updated documentation for new trident release #79

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e88a2dc
added info on new bibliography Web-API
stschiff Jan 10, 2025
c04273f
more updates to md
stschiff Jan 10, 2025
d9f6c64
technical setup for new trident version
nevrome Jan 17, 2025
59749ef
update of rectify
nevrome Jan 17, 2025
d536713
documentation for the new --bibliography option
nevrome Jan 17, 2025
395b6e5
update of command line docu
nevrome Jan 17, 2025
f2789f1
minimal documentation for --zip
nevrome Jan 17, 2025
4331f73
typos
nevrome Jan 17, 2025
b66d3f2
minimal documentation for the gzipped storage of genotype data
nevrome Jan 17, 2025
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16 changes: 9 additions & 7 deletions genotype_data.md
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Expand Up @@ -6,12 +6,14 @@ Genotype data in Poseidon packages can be stored in either of two (multi)file fo

| | PLINK (binary) | EIGENSTRAT |
|---|---|---|
| genotype file | [`.bed` (binary biallelic genotype table)](https://www.cog-genomics.org/plink/1.9/formats#bed) | [`.geno` (genotype file)](https://github.com/DReichLab/EIG/blob/fb4fb59065055d3622e0f97f0149588eae630a3e/CONVERTF/README#L67)
| SNP file | [`.bim` (extended MAP file)](https://www.cog-genomics.org/plink/1.9/formats#bim) | [`.snp` (snp file)](https://github.com/DReichLab/EIG/blob/fb4fb59065055d3622e0f97f0149588eae630a3e/CONVERTF/README#L67) |
| genotype file | [`.bed` (binary biallelic genotype table)](https://www.cog-genomics.org/plink/1.9/formats#bed) or `.bed.gz` | [`.geno` (genotype file)](https://github.com/DReichLab/EIG/blob/fb4fb59065055d3622e0f97f0149588eae630a3e/CONVERTF/README#L67) or `.geno.gz`
| SNP file | [`.bim` (extended MAP file)](https://www.cog-genomics.org/plink/1.9/formats#bim) or `.bim.gz` | [`.snp` (snp file)](https://github.com/DReichLab/EIG/blob/fb4fb59065055d3622e0f97f0149588eae630a3e/CONVERTF/README#L67) or `.snp.gz` |
| individual file | [`.fam` (sample information)](https://www.cog-genomics.org/plink/1.9/formats#fam) | [`.ind` (indiv file)](https://github.com/DReichLab/EIG/blob/fb4fb59065055d3622e0f97f0149588eae630a3e/CONVERTF/README#L67) |

The PLINK file format is a well specified, storage efficient data type compatible with many bioinformatic software tools, which made it an obvious choice for Poseidon. The EIGENSTRAT format is also common within archaeogenetics, compatible with many of the important tools developed by the Reich Lab, e.g. the ones in the [EIGENSOFT](https://github.com/DReichLab/EIG) and [ADMIXTOOLS](https://github.com/DReichLab/AdmixTools). In the future even more formats might be supported (see e.g. [here](https://reich.hms.harvard.edu/software/InputFileFormats)).

The large genotype data files to store SNP definitions and values can be stored in gzipped files (`*.gz`).

The `genotypeData` field in the `POSEIDON.yml` file documents in which format the data for a package is stored and the relative paths to the respective files.

<table>
Expand All @@ -25,8 +27,8 @@ The `genotypeData` field in the `POSEIDON.yml` file documents in which format th
```
genotypeData:
format: PLINK
genoFile: X.bed
snpFile: X.bim
genoFile: X.bed | X.bed.gz
snpFile: X.bim | X.bim.gz
indFile: X.fam
snpSet: 1240K
```
Expand All @@ -36,9 +38,9 @@ genotypeData:
```
genotypeData:
format: EIGENSTRAT
genoFile: X.geno
snpFile: X.snp
indFile: X.indiv
genoFile: X.geno | X.geno.gz
snpFile: X.snp | X.snp.gz
indFile: X.ind
snpSet: 1240K
```
</td>
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1 change: 1 addition & 0 deletions pdf_conversion/pdf_conversion_list.tsv
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Expand Up @@ -12,6 +12,7 @@ trident_guide_archive/trident_guide_1.3.0.4.md trident_guide_archive/trident_gui
trident_guide_archive/trident_guide_1.4.0.2_to_1.4.0.3.md trident_guide_archive/trident_guide_1.4.0.2_to_1.4.0.3.pdf
trident_guide_archive/trident_guide_1.4.1.0_to_1.5.0.1.md trident_guide_archive/trident_guide_1.4.1.0_to_1.5.0.1.pdf
trident_guide_archive/trident_guide_1.5.4.0.md trident_guide_archive/trident_guide_1.5.4.0.pdf
trident_guide_archive/trident_guide_1.5.7.0_to_1.5.7.3.md trident_guide_archive/trident_guide_1.5.7.0_to_1.5.7.3.pdf
xerxes_guide_archive/xerxes_guide_0.2.0.0.md xerxes_guide_archive/xerxes_guide_0.2.0.0.pdf
xerxes_guide_archive/xerxes_guide_1.0.0.2.md xerxes_guide_archive/xerxes_guide_1.0.0.2.pdf
janno_details.md janno_details.pdf
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