poseidon-framework poseidon-schema issues

poseidon-framework / poseidon-schema

An archaeogenetic genotype data organisation file format

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[Review recommendation] Add a .janno colum to document the broad chronological era of a sample

#83 nevrome opened 3 months ago
4
[Review recommendation] Add a .janno column for the institution curating the archaeological remains for a sample

#82 nevrome opened 3 months ago
2
[Review recommendation] Introduce an explicit .janno column for sex chromosome aneuploidies

#81 nevrome opened 3 months ago
4
[Review recommendation] Make Poseidon explicitly species-agnostic

#80 nevrome opened 3 months ago
3
[Review recommendation] Document the reference genome used for each sample

#79 nevrome opened 3 months ago
6
[Review recommendation] Integrate universal sample IDs provided by the BioSamples database

#78 nevrome opened 3 months ago
2
How to support multiple SNP-sets

#77 stschiff opened 3 months ago
1
Reevaluate haplogroup .janno columns

#76 nevrome opened 5 months ago
6
New column `Source_Material`

#75 stschiff opened 5 months ago
0
Introduce Individual_Id

#74 stschiff opened 5 months ago
0
Specify sex determination variables `RateX`, `RateY`, `RateErrX`, `RateErrY`

#73 nevrome opened 7 months ago
3
Small improvements to the 2.7.1 schema text

#72 nevrome closed 7 months ago
2
PDF version of the schema

#71 nevrome closed 7 months ago
0
Package versioning

#70 nevrome closed 7 months ago
8
Clarify versioning rules

#69 stschiff closed 7 months ago
0
Clarification for the meaning of the Date_Type column

#68 nevrome closed 9 months ago
1
Allowing multiple values for Damage

#67 AyGhal opened 9 months ago
7
Capture_Type should not contain "ReferenceGenome"

#66 stschiff opened 1 year ago
0
Update POSEIDON_yml_fields.tsv

#65 stschiff closed 1 year ago
0
Contamination column schema overly restrictive?

#64 stschiff closed 1 year ago
3
Rephrasing

#63 nevrome closed 1 year ago
2
Update README.md

#62 stschiff closed 1 year ago
2
SSF: `sample_accession` and `secondary_sample_accession` should not have a *unique* constraint

#61 nevrome closed 1 year ago
4
Changes for Poseidon v2.7.1

#60 TCLamnidis closed 1 year ago
1
SSF: `library_name` field description needs updating.

#59 TCLamnidis closed 1 year ago
0
Additional columns for ENA tables

#58 TCLamnidis closed 1 year ago
8
suggestions for additional changes in 2.7.0

#57 nevrome closed 1 year ago
6
Poseidon v2.7.0

#56 nevrome closed 1 year ago
11
Linking raw data from ENA

#55 stschiff closed 1 year ago
3
added Twist and Arbor capture types

#54 stschiff closed 1 year ago
5
Individual_ID vs. Poseidon_ID

#53 xrotwang closed 2 years ago
4
Twist capture array

#52 nevrome closed 1 year ago
3
Poseidon v2.6.0

#51 nevrome closed 1 year ago
2
Coverage_1240K should probably be renamed to Coverage_on_autosomal_targets

#50 stschiff closed 2 years ago
1
Add anthropological fields?

#49 stschiff opened 2 years ago
0
Include `Date_note`?

#48 stschiff closed 2 years ago
1
Autosomal contamination columns, like autContam_contamLD

#47 stschiff closed 2 years ago
1
rename xContam to xContam_ANGSD

#46 stschiff closed 2 years ago
1
Support for genotype data in VCF format

#45 nevrome opened 2 years ago
1
Specification of floating point number notation

#44 nevrome opened 2 years ago
1
changes for Poseidon 2.5.0

#42 nevrome closed 2 years ago
17
Maybe "outsource" the checksums by turning the package into a "bagit" package

#41 xrotwang opened 3 years ago
0
Country could be specified more specifically

#40 xrotwang closed 1 year ago
15
Identifiers

#43 xrotwang closed 2 years ago
5
made snpSet non-mandatory, also changed README

#39 stschiff closed 3 years ago
1
Make `snpSet` optional

#38 stschiff closed 3 years ago
0
More clearly define meaning of `Coverage_1240k`

#37 stschiff closed 2 years ago
1
Change `Data_Type` to `Capture_Type`?

#36 stschiff closed 2 years ago
4
Source accession update

#35 stschiff closed 3 years ago
12
The Publication_Status .janno column should support multiple entries

#34 nevrome closed 3 years ago
2