Another capture type and some documentation on the individual protocols

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).
+- `Carpenter2013`: 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.

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 `Carpenter2013` to `Capture_Type`.
 
 ##### Removed columns
 

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;Carpenter2013;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