diff --git a/README.md b/README.md index 520bafb..017727a 100644 --- a/README.md +++ b/README.md @@ -229,3 +229,16 @@ The `.ssf` file is another tab-separated text file with a header line. It stores - If information is unknown or a variable does not apply, then the respective cell(s) MAY be filled with `n/a` or simply an empty string. - Multiple predefined columns of the `.ssf` file are list columns that can hold multiple values (either strings or numerics) separated by `;`. - The decimal separator for all floating point numbers MUST be `.`. + +### Details + +#### The `Capture_Type` .janno column + +The following protocols are specified: + +- `Shotgun`: Sequencing without any enrichment (whole genome sequencing, screening etc.). +- `1240K`: Target enrichment with hybridization capture optimised for sequences covering the 1240k SNP array, see [@Fu2015](https://doi.org/10.1038/nature14558), [@Haak2015](https://doi.org/10.1038/nature14317), [@Mathieson2015](https://doi.org/10.1038/nature16152). +- `ArborComplete`, `ArborPrimePlus`, `ArborAncestralPlus`: Target enrichment with hybridization capture as provided by Arbor Biosciences in three different kits branded [myBaits Expert Human Affinities](https://arborbiosci.com/genomics/targeted-sequencing/mybaits/mybaits-expert/mybaits-expert-human-affinities). +- `TwistAncientDNA`: Target enrichment with hybridization capture as provided by Twist Bioscience [@Rohland2022](https://doi.org/10.1101/gr.276728.122). +- `WISC2013`: Whole genome capture as described by [@Carpenter2013](10.1016/j.ajhg.2013.10.002). +- `OtherCapture`: Target enrichment with hybridization capture for any other set of sequences. diff --git a/changelog.md b/changelog.md index 95e1198..6cefcc2 100644 --- a/changelog.md +++ b/changelog.md @@ -43,6 +43,7 @@ - Changed the scaling of the columns `Endogenous` and `Damage` from percent (0-100) to fractions (0-1). - Allowed multiple values in the `Damage` column for estimates per library. - Slightly adjusted the definitions of `MT_Haplogroup` and `Y_Haplogroup` to better account for non-human data. +- Added the option `WISC2013` to `Capture_Type`. ##### Removed columns diff --git a/janno_columns.tsv b/janno_columns.tsv index ee24c70..0f9f3d0 100644 --- a/janno_columns.tsv +++ b/janno_columns.tsv @@ -32,7 +32,7 @@ Y_Haplogroup Y-chromosome haplogroup derived for the sample. For human data this Source_Material sampled material, multiple entries separated by ; String TRUE TRUE FALSE petrous;bone;tooth;hair;soft;sediment;other FALSE FALSE Nr_Libraries number of libraries produced for the sample Integer FALSE FALSE FALSE FALSE FALSE Library_Names identifiers of the libraries used to generate the genotype data for the sample, multiple values separated by ; String TRUE FALSE FALSE FALSE FALSE -Capture_Type capture method for the individual libraries generated for the sample, multiple values separated by ; String TRUE TRUE FALSE Shotgun;1240K;ArborComplete;ArborPrimePlus;ArborAncestralPlus;TwistAncientDNA;OtherCapture FALSE FALSE +Capture_Type capture method for the individual libraries generated for the sample, multiple values separated by ; String TRUE TRUE FALSE Shotgun;1240K;ArborComplete;ArborPrimePlus;ArborAncestralPlus;TwistAncientDNA;WISC2013;OtherCapture FALSE FALSE UDG udg treatment for the libraries, mixed in case multiple libraries with different UDG treatment were merged String FALSE TRUE FALSE minus;half;plus;mixed FALSE FALSE Library_Built strandedness of the libraries, “mixed” in case multiple libraries with different protocols were merged String FALSE TRUE FALSE ds;ss;mixed FALSE FALSE Genotype_Ploidy ploidy of the genotypes for the sample String FALSE TRUE FALSE diploid;haploid FALSE FALSE