split 2018_BostonDatashare_modern_published into publication-wise pac…

…kages - and merged these with the respective ones from the ancient repo

2012_MeyerScience/2012_MeyerScience.bib

@@ -0,0 +1,20 @@
+@article{MeyerScience2012,
+ title={A High-Coverage Genome Sequence from an Archaic Denisovan Individual},
+ volume={338},
+ url={https://doi.org/10.1126/science.1224344},
+ DOI={10.1126/science.1224344},
+ number={6104},
+ journal={Science},
+ publisher={American Association for the Advancement of Science (AAAS)},
+ author={Meyer, M. and Kircher, M. and Gansauge, M.-T. and Li, H. and Racimo, F. and Mallick, S. and Schraiber, J. G. and Jay, F. and Prufer, K. and Filippo, C. de and Sudmant, P. H. and Alkan, C. and Fu, Q. and Do, R. and Rohland, N. and Tandon, A. and Siebauer, M. and Green, R. E. and Bryc, K. and Briggs, A. W. and Stenzel, U. and Dabney, J. and Shendure, J. and Kitzman, J. and Hammer, M. F. and Shunkov, M. V. and Derevianko, A. P. and Patterson, N. and Andres, A. M. and Eichler, E. E. and Slatkin, M. and Reich, D. and Kelso, J. and Paabo, S.},
+ year={2012},
+ month={8},
+ pages={222–226}
+}
+
+@misc{AADR_2019,
+ title = {Allen Ancient {DNA} Resource ({AADR)}: Downloadable genotypes of present-day and ancient {DNA} data, version 37.2},
+ year = 2019,
+ url = {https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data},
+ howpublished = {\url{https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data}}
+}

2012_MeyerScience/2012_MeyerScience.fam

@@ -0,0 +1,6 @@
+Ignore_Mbuti(discovery).DG A_Mbuti-5.DG 0 0 1 0
+Ignore_Yoruba(discovery).DG A_Yoruba-4.DG 0 0 1 0
+Ignore_Sardinian(discovery).DG A_Sardinian-4.DG 0 0 1 0
+Ignore_French(discovery).DG A_French-4.DG 0 0 1 0
+Dinka.DG A_Dinka-4.DG 0 0 1 0
+Ignore_Ju_hoan_North(discovery).DG A_Ju_hoan_North-5.DG 0 0 1 0

2012_MeyerScience/2012_MeyerScience.janno

@@ -0,0 +1,7 @@
+Individual_ID Collection_ID Source_Tissue Country Location Site Latitude Longitude Date_C14_Labnr Date_C14_Uncal_BP Date_C14_Uncal_BP_Err Date_BC_AD_Median Date_BC_AD_Start Date_BC_AD_Stop Date_Type No_of_Libraries Data_Type Genotype_Ploidy Group_Name Genetic_Sex Nr_autosomal_SNPs Coverage_1240K MT_Haplogroup Y_Haplogroup Endogenous UDG Library_Built Damage Xcontam Xcontam_stderr mtContam mtContam_stderr Primary_Contact Publication_Status Note Keywords
+A_Mbuti-5.DG HGDP00456 n/a Congo n/a n/a 1.0 29.0 n/a n/a n/a n/a n/a n/a modern n/a Shotgun diploid Ignore_Mbuti(discovery).DG M 593057 24.34 n/a n/a n/a n/a ds n/a n/a n/a n/a n/a n/a MeyerScience2012 PASS n/a
+A_Yoruba-4.DG HGDP00927 n/a Nigeria n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a modern n/a Shotgun diploid Ignore_Yoruba(discovery).DG M 593097 32.12 n/a n/a n/a n/a ds n/a n/a n/a n/a n/a n/a MeyerScience2012 PASS n/a
+A_Sardinian-4.DG HGDP00665 n/a Italy n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a modern n/a Shotgun diploid Ignore_Sardinian(discovery).DG M 593109 24.68 n/a n/a n/a n/a ds n/a n/a n/a n/a n/a n/a MeyerScience2012 PASS n/a
+A_French-4.DG HGDP00521 n/a France n/a n/a 46.0 2.0 n/a n/a n/a n/a n/a n/a modern n/a Shotgun diploid Ignore_French(discovery).DG M 592535 26.73 n/a n/a n/a n/a ds n/a n/a n/a n/a n/a n/a MeyerScience2012 PASS n/a
+A_Dinka-4.DG A_Dinka-4 n/a Sudan Aweil n/a 8.78333 27.4 n/a n/a n/a n/a n/a n/a modern n/a Shotgun diploid Dinka.DG M 593076 27.98 n/a n/a n/a n/a ds n/a n/a n/a n/a n/a n/a MeyerScience2012 PASS n/a
+A_Ju_hoan_North-5.DG HGDP01029 n/a Namibia n/a n/a -18.93726 21.45245 n/a n/a n/a n/a n/a n/a modern n/a Shotgun diploid Ignore_Ju_hoan_North(discovery).DG M 593045 32.74 n/a n/a n/a n/a ds n/a n/a n/a n/a n/a n/a MeyerScience2012 PASS n/a

2012_MeyerScience/POSEIDON.yml

@@ -0,0 +1,19 @@
+poseidonVersion: 2.1.0
+title: 2012_MeyerScience
+description: This package was initially constructed based on the Allen Ancient DNA
+ Resource (https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data,
+ version 37.2)
+contributor:
+- name: Ayshin Ghalichi
+ email: ghalichi@shh.mpg.de
+- name: Clemens Schmid
+ email: schmid@shh.mpg.de
+packageVersion: 1.0.0
+lastModified: 2021-03-18
+genotypeData:
+ format: PLINK
+ genoFile: 2012_MeyerScience.bed
+ snpFile: 2012_MeyerScience.bim
+ indFile: 2012_MeyerScience.fam
+jannoFile: 2012_MeyerScience.janno
+bibFile: 2012_MeyerScience.bib

2012_PattersonGenetics/2012_PattersonGenetics.bib

@@ -0,0 +1,20 @@
+@article{PattersonGenetics2012,
+ title={Ancient Admixture in Human History},
+ volume={192},
+ url={https://doi.org/10.1534/genetics.112.145037},
+ DOI={10.1534/genetics.112.145037},
+ number={3},
+ journal={Genetics},
+ publisher={Oxford University Press (OUP)},
+ author={Patterson, Nick and Moorjani, Priya and Luo, Yontao and Mallick, Swapan and Rohland, Nadin and Zhan, Yiping and Genschoreck, Teri and Webster, Teresa and Reich, David},
+ year={2012},
+ month={9},
+ pages={1065–1093}
+}
+
+@misc{AADR_2019,
+ title = {Allen Ancient {DNA} Resource ({AADR)}: Downloadable genotypes of present-day and ancient {DNA} data, version 37.2},
+ year = 2019,
+ url = {https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data},
+ howpublished = {\url{https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data}}
+}