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1 | | -janno_column_name description column_type choice_options mandatory range_lower range_upper |
2 | | -Individual_ID String TRUE |
3 | | -Collection_ID String TRUE |
4 | | -Source_Tissue skeletal/tissue/source elements, multiple values separated by ; in case of merged libraries String list FALSE |
5 | | -Country present-day political country String FALSE |
6 | | -Location city or village nearby the site String FALSE |
7 | | -Site site name String FALSE |
8 | | -Latitude latitude with up to 5 places after the decimal point Float FALSE -90 90 |
9 | | -Longitude longitude with up to 5 places after the decimal point Float FALSE -180 180 |
10 | | -Date_C14_Labnr labnr of C14 date, multiple values in case of multiple dates String list FALSE |
11 | | -Date_C14_Uncal_BP uncalibrated years BP (as in before 1950AD), as reported by C14 labs, multiple values separated by ; in the same order as Date_C14_Labnr in case of multiple dates Integer list FALSE 0 Inf |
12 | | -Date_C14_Uncal_BP_Err standard deviation (1 sigma ±), as reported by C14 labs, multiple values separated by ; in the same order as Date_C14_Labnr in case of multiple dates Integer list FALSE 0 Inf |
13 | | -Date_BC_AD_Median calibrated median age for C14 dates, or simple mid-points for archaeological intervals, 2000 for modern samples Integer FALSE -Inf 2050 |
14 | | -Date_BC_AD_Start lower (older) bound for the age, negative numbers for BC, positive numbers for AD, in case of C14 dates 95% interval post calibration, 2000 for modern samples Integer FALSE -Inf 2050 |
15 | | -Date_BC_AD_Stop upper (more recent) bound for the age, negative numbers for BC, positive numbers for AD, in case of C14 dates 95% interval post calibration, 2000 for modern samples Integer FALSE -Inf 2050 |
16 | | -Date_Type """C14"" if directly from the individual, ""contextual"" if based on archaeology or other C14 dates from the site, “modern” for present-day individuals" String choice C14;contextual;modern FALSE |
17 | | -No_of_Libraries number of libraries Integer FALSE |
18 | | -Data_Type String choice Shotgun;1240K;OtherCapture;ReferenceGenome FALSE |
19 | | -Genotype_Ploidy String choice diploid;haploid FALSE |
20 | | -Group_Name ideally Eisenmann rule + underscore flags, e.g. to annotate relatives or outliers or low coverage, multiple entries separated by ; to accommodate different labels String list FALSE |
21 | | -Genetic_Sex """F"", ""M"" or ""U"" because eigenstrat and plink formats only support these three. Edge cases (XXY, XYY, X0) are undefined and should be grouped as F, M or U, with a note added" Char choice F;M;U FALSE |
22 | | -Nr_autosomal_SNPs number of autosomal SNPs covered for 1240K capture or SG data pulldown Integer FALSE |
23 | | -Coverage_1240K average X-fold coverage across 1240K SNP sites after quality filtering (internal data), NOT the % SNPs of 1.2M possible Float FALSE |
24 | | -MT_Haplogroup mitochondrial haplogroup after phylotree.org as reported by Haplofind or Haplogrep String FALSE |
25 | | -Y_Haplogroup Y-chromosome haplogroup reported as published, for internal data, please follow syntax with main branch + most terminal derived Y-SNP (e.g. R1b-P312) String FALSE |
26 | | -Endogenous % endogenous DNA for the SG libraries, as estimated by EAGER for the best library (in percent), not on target and no quality filter Float FALSE 0 100 |
27 | | -UDG “mixed” in case multiple libraries with different UDG treatment were merged String choice minus;half;plus;mixed FALSE |
28 | | -Library_Built “ds” for double stranded, “ss” for single stranded String choice ds;ss;other FALSE |
29 | | -Damage % damage on 5' end for the main shotgun library used for sequencing and/or capture Float FALSE 0 100 |
30 | | -Xcontam if male for captured library Float FALSE 0 1 |
31 | | -Xcontam_stderr standard error of ANGSD X contamination estimate Float FALSE 0 Inf |
32 | | -mtContam mitochondrial contamination rate as estimated by ContamMix and/or Schmutzi Float FALSE 0 1 |
33 | | -mtContam_stderr Standard error of ContamMix/Schmutzi estimate Float FALSE 0 Inf |
34 | | -Primary_Contact Project lead or first author String FALSE |
35 | | -Publication_Status """AuthorYearJournal"" or ""unpublished""" String FALSE |
36 | | -Note wildcard comments. e.g. note down aneuploidies here String FALSE |
| 1 | +janno_column_name description column_type choice_options mandatory unique range_lower range_upper |
| 2 | +Individual_ID id as defined by the genetics laboratory, needs to be unique (e.g. I1234, BOT001), if multiple datasets exist for the same individual different IDs are required (e.g. loschbour_snpAD) String TRUE TRUE |
| 3 | +Collection_ID id as defined by the provider/owner of a sample (e.g. grave 40 skeleton 2) String FALSE FALSE |
| 4 | +Source_Tissue skeletal/tissue/source elements, multiple values separated by ; in case of merged libraries String list FALSE FALSE |
| 5 | +Country present-day political country String FALSE FALSE |
| 6 | +Location city or village nearby the site String FALSE FALSE |
| 7 | +Site site name String FALSE FALSE |
| 8 | +Latitude latitude with up to 5 places after the decimal point Float FALSE FALSE -90 90 |
| 9 | +Longitude longitude with up to 5 places after the decimal point Float FALSE FALSE -180 180 |
| 10 | +Date_C14_Labnr labnr of C14 date, multiple values in case of multiple dates String list FALSE FALSE |
| 11 | +Date_C14_Uncal_BP uncalibrated years BP (as in before 1950AD), as reported by C14 labs, multiple values separated by ; in the same order as Date_C14_Labnr in case of multiple dates Integer list FALSE FALSE 0 Inf |
| 12 | +Date_C14_Uncal_BP_Err standard deviation (1 sigma ±), as reported by C14 labs, multiple values separated by ; in the same order as Date_C14_Labnr in case of multiple dates Integer list FALSE FALSE 0 Inf |
| 13 | +Date_BC_AD_Median calibrated median age for C14 dates, or simple mid-points for archaeological intervals, 2000 for modern samples Integer FALSE FALSE -Inf 2050 |
| 14 | +Date_BC_AD_Start lower (older) bound for the age, negative numbers for BC, positive numbers for AD, in case of C14 dates 95% interval post calibration, 2000 for modern samples Integer FALSE FALSE -Inf 2050 |
| 15 | +Date_BC_AD_Stop upper (more recent) bound for the age, negative numbers for BC, positive numbers for AD, in case of C14 dates 95% interval post calibration, 2000 for modern samples Integer FALSE FALSE -Inf 2050 |
| 16 | +Date_Type """C14"" if directly from the individual, ""contextual"" if based on archaeology or other C14 dates from the site, “modern” for present-day individuals" String choice C14;contextual;modern FALSE FALSE |
| 17 | +No_of_Libraries number of libraries Integer FALSE FALSE |
| 18 | +Data_Type specifics of data generation method String choice Shotgun;1240K;OtherCapture;ReferenceGenome FALSE FALSE |
| 19 | +Genotype_Ploidy ploidy of the genotypes String choice diploid;haploid FALSE FALSE |
| 20 | +Group_Name ideally Eisenmann rule + underscore flags, e.g. to annotate relatives or outliers or low coverage, multiple entries separated by ; to accommodate different labels, in case of multiple entries the first one must equal the group name in the .fam file String list TRUE FALSE |
| 21 | +Genetic_Sex """F"", ""M"" or ""U"" because eigenstrat and plink formats only support these three. Edge cases (XXY, XYY, X0) are undefined and should be grouped as F, M or U, with a note added" Char choice F;M;U TRUE FALSE |
| 22 | +Nr_autosomal_SNPs number of autosomal SNPs covered for 1240K capture or SG data pulldown Integer FALSE FALSE |
| 23 | +Coverage_1240K average X-fold coverage across 1240K SNP sites after quality filtering (internal data), NOT the % SNPs of 1.2M possible Float FALSE FALSE |
| 24 | +MT_Haplogroup mitochondrial haplogroup after phylotree.org as reported by Haplofind or Haplogrep String FALSE FALSE |
| 25 | +Y_Haplogroup Y-chromosome haplogroup reported as published, for internal data, please follow syntax with main branch + most terminal derived Y-SNP (e.g. R1b-P312) String FALSE FALSE |
| 26 | +Endogenous % endogenous DNA for the SG libraries, as estimated by EAGER for the best library (in percent), not on target and no quality filter Float FALSE FALSE 0 100 |
| 27 | +UDG “mixed” in case multiple libraries with different UDG treatment were merged String choice minus;half;plus;mixed FALSE FALSE |
| 28 | +Library_Built “ds” for double stranded, “ss” for single stranded String choice ds;ss;other FALSE FALSE |
| 29 | +Damage % damage on 5' end for the main shotgun library used for sequencing and/or capture Float FALSE FALSE 0 100 |
| 30 | +Xcontam if male for captured library Float FALSE FALSE 0 1 |
| 31 | +Xcontam_stderr standard error of ANGSD X contamination estimate Float FALSE FALSE 0 Inf |
| 32 | +mtContam mitochondrial contamination rate as estimated by ContamMix and/or Schmutzi Float FALSE FALSE 0 1 |
| 33 | +mtContam_stderr Standard error of ContamMix/Schmutzi estimate Float FALSE FALSE 0 Inf |
| 34 | +Primary_Contact Project lead or first author String FALSE FALSE |
| 35 | +Publication_Status "bibtex key (e.g. ""@AuthorYearJournal"") or ""unpublished""" String FALSE FALSE |
| 36 | +Note wildcard comments. e.g. note down aneuploidies here String FALSE FALSE |
| 37 | +Keywords Arbitrary tags separated by ; (e.g. for custom sorting purposes) String list FALSE FALSE |
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