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| # genotypes_loader | ||
| # Genotypes Loader | ||
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| This module provides a drush command to load genotypic data from a variety of file formats. Data is saved in GMOD Chado with three separate methods supported (See Data Storage below). | ||
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| ## Command | ||
| - Command: load-genotypes | ||
| - Alias: load-geno | ||
| - Arguments: | ||
| - input-file: The filename of the matrix file for upload | ||
| - sample-file: The filename of a tab-delimited file specifying for each sample name in the genotypes file: the name of the stock in the database, the stock accession ID, the name of the germplasm, and the germplasm Accession ID. See "samples.list" in the sample_files folder. | ||
| - Options: | ||
| - variant-type: The Sequence Ontology (SO) term name that describes the type of variants in the file (eg. SNP, MNP, indel). | ||
| - marker-type: The Sequence Ontology (SO) term name that describes the marker technology used to generate the genotypes in the file (e.g. "Exome Capture", "GBS", "KASPar", etc.). | ||
| - ndgeolocation: A meaningful location associated with this natural diversity experiment. For example, this could be the location the assay was completed in, the location the germplasm collection was from, or the location the markers were developed at. This should be the description field of your ndgeolocation. | ||
| - organism: The organism to which the genotypes are associated with. | ||
| - project-name: All genotypes will be grouped via a project to allow users to specify a particular dataset. | ||
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| **This loader supports 3 different file formats (described under file formats below) and will auto-detect which format you have provided.** | ||
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| Example Usage: | ||
| - Load a genotype matrix file (mymatrix.tsv) using the sample/germplasm information provided in samples.list. With this example, you will be prompted to enter each of the options listed above. | ||
| - `drush load-genotypes mymatrix.tsv samples.list` | ||
| - Load a VCF file (mygenotypes.vcf) using the sample/germplasm information provided in samples.list but provide the command with all the options upfront to avoid prompting. | ||
| - `drush load-genotypes mygenotypes.vcf samples.list --organism="Lens culinaris" --variant-type="SNP" --marker-type="genetic_marker" --project-name="My SNP Discovery Project" --ndgeolocation="here"` | ||
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| ## File Formats | ||
| This module supports loading of three types of genotype files: | ||
| - VCF | ||
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| ``` | ||
| ##fileformat=VCFv4.0 | ||
| ##fileDate=20090805 | ||
| ##source=myImputationProgramV3.1 | ||
| ##reference=1000GenomesPilot-NCBI36 | ||
| ##phasing=partial | ||
| ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> | ||
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> | ||
| ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> | ||
| ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> | ||
| ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> | ||
| ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> | ||
| ##FILTER=<ID=q10,Description="Quality below 10"> | ||
| ##FILTER=<ID=s50,Description="Less than 50% of samples have data"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | ||
| ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Ross Prado Ash | ||
| 1A 14370 . G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. | ||
| 1A 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 | ||
| 1A 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 | ||
| 1A 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 | ||
| 1A 11111 1subfield C A 50 PASS A=1;B=2;C=3 GT 0/1 ./. 1/1 | ||
| ``` | ||
| - Genotype Matrix: a tab-delimited data file where each line corresponds to a SNP and columns correspond to germplasm assayed. Expected columns: (1) Marker Name, (2) Chromosome Name, (3) Position on Chromosome, (4+) Sample Genotype Calls. | ||
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| ``` | ||
| Marker name Chromosome Position 1048-8R 964a-46 Giftgi | ||
| FcChr1Ap11111 1A 11111 CC AC AA | ||
| FcChr1Ap22222 1A 22222 GG GC GG | ||
| FcChr1Ap33333 1A 33333 TA AA GA | ||
| ``` | ||
| - Genotype Flat-file: a tab delimited data file where each line is a genotypic call. Expected columns: (1) Marker name, (2) Chromosome Name, (3) Position on Chromosome, (4) Sample Name, (5) Genotype call. | ||
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| ``` | ||
| Marker name Chromosome Position Sample name Genotype call | ||
| FcChr1Ap11111 1A 11111 Ross CC | ||
| FcChr1Ap11111 1A 11111 Prado CC | ||
| FcChr1Ap11111 1A 11111 Ash CC | ||
| FcChr1Ap11111 1A 11111 Piero CT | ||
| FcChr1Ap11111 1A 11111 Tai CC | ||
| FcChr1Ap11111 1A 11111 Beverly TC | ||
| FcChr1Ap11111 1A 11111 Argent CC | ||
| FcChr1Ap11111 1A 11111 Trenus TT | ||
| FcChr1Ap11111 1A 11111 Zapelli CC | ||
| FcChr1Ap11111 1A 11111 Amato CG | ||
| ``` | ||
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| All formats require a separate samples file describing the germplasm assayed. This file is expected to be a tab-delimited file with the following columns: (1) Sample Name in File, (2) Sample name, (3) Sample Accession, (4) Germplasm name, (5) Germplasm Accession. | ||
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| ``` | ||
| Sample_name Sample_name Sample_Accession Germplasm_name Germplasm_Accession | ||
| Ross Ross_110201 Catsam1 Ross Catgerm1 | ||
| Prado Prado_110201 Catsam2 Prado Catgerm2 | ||
| Ash Ash_110201 Catsam3 Ash Catgerm3 | ||
| Piero Piero_110201 Catsam4 Piero Catgerm4 | ||
| Tai Tai_110201 Catsam5 Tai Catgerm5 | ||
| Beverly Beverly_110201 Catsam6 Beverly Catgerm6 | ||
| Argent Argent_110201 Catsam7 Argent Catgerm7 | ||
| Trenus Trenus_110201 Catsam8 Trenus Catgerm8 | ||
| Zapelli Zapelli_110201 Catsam9 Zapelli Catgerm9 | ||
| Amato Amato_110201 Catsam10 Amato Catgerm10 | ||
| ``` | ||
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| ## Data Storage | ||
| Genotypes loaded by this module can be stored in chado in via one of the following admin selected methods: | ||
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| | Method | Name | Custom Tables | Supports Meta-data | # Tables | Comments | | ||
| |--------|----------------|---------------|--------------------|----------|---------------------------------------------------------------------------------------------------------------------------------------------------| | ||
| | 1 | ND Experiment | No | Yes | 14 | Not suitable beyond 3 million genotype calls. | | ||
| | 2 | Genotype Call | Yes | Yes | 10 | Most efficient; although it touches the same number of tables as Method #3 there are less records per genotype call. | | ||
| | 3 | Stock Genotype | No | No | 10 | A good alternative if you don't want to use custom tables but have a lot of data. Similar efficiency to Method #2 but less support for meta-data. | | ||
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| For more information see [ND Genotypes: How to Store your Data](https://github.com/UofS-Pulse-Binfo/nd_genotypes/wiki/How-to-Store-your-Data). | ||
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| This module currently expects the following controlled vocabulary terms already exist in chado: | ||
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| | Term Name | Controlled Vocabulary | | ||
| |---------------------|-----------------------| | ||
| | DNA | stock_type | | ||
| | Accession | stock_type | | ||
| | Individual | stock_type | | ||
| | is_extracted_from | stock_relationship | | ||
| | is_marker_of | stock_relationship | | ||
| | *Indicated by user* | sequence | | ||
| | *Indicated by user* | sequence | | ||
| | marker_type | feature_property | | ||
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| In the future, you will be able to configure these terms through a settings form under module configuration. |