This plugin scores all discovered SNPs for various coverage, depth and genotypic statistics for a given set of taxa. If no taxa are specified, the plugin will score all taxa currently stored in the data base. If no taxa file is specified, the plugin uses the taxa stored in the database.

The parameters to this plugin are:

• -db <Output Database file> : Name of output file (e.g. GBSv2.db) (REQUIRED)
• -deleteOldData <true | false> : Delete existing SNP quality data from db tables. If true, SNP quality data is cleared from the snpQuality table in the database before adding new data. (Default: true)
• -taxa <Taxa sublist file> : Name of taxa list input file in taxa list format. If no taxa file is specified, all taxa from the master list are used to calculate the quality metrics. By using taxa sublist files, the user can store quality metrics for different subsets of the taxa concurrently in the data base.
• -tname <Taxa set name > : Name of taxa set for database. This allows the user to identify quality metrics that were run for a specific set of taxa. The tname parameter should be used if a subset of taxa is specified in a taxa list file. This allows for identifying the quality metrics calculated for a specific subset of taxa. The default name used when none is supplied is "ALL".
• -statFile <Quality information output name > : Name of the output file containing the quality statistics in a tab delimited format.

A description of the data contained in the output file:

• aveDepth: Average taxon read depth at SNP.
• minorDepthProp – the percentage of total depth consisting of minor allele 1
• minorDepthProp2 – the percentage of total depth consisting of minor allele 2
• gapDepthProp – percentage of the total depth that represents a gap (allele = GAP_ALLELE, gapDepth/total_depths)
• propCovered – proportion of taxa with depth > 0 at SNP
• propCovered2 – proportion of taxa with depth > 1 at SNP
• taxaCntWithMinorAlleleGE2 – number of taxa containing the minor allele 1 at depth > 1

If there is more than one allele, the following output is included:

• genotypeCnt: total number of taxa with a depth > 1
• minorAlleleFreqGE2 – minor allele frequency calculated from the taxa with depth > 1
• hetFreq_DGE2 – number of taxa with a depth > 1 that appear heterozygous
• inbredF_DGE2 – inbreeding coefficient for tax with depth > 1, calculated as: 1 - (proportion hets/expected heterozygosity)

To run this command from the command line:

#!java

./run_pipeline.pl -fork1 -SNPQualityProfilerPlugin
-db /Users/lcj34/development/GBS/GBSv2.db
-taxa /Users/lcj34/development/files/IBMGBSTaxalist.txt
-tname "IBM" -statFile "outputStats.txt" -deleteOldData true -endPlugin -runfork1

To call SNPQualityProfilerPlugin from program code :

#!java

        new SNPQualityProfilerPlugin()
                .dBFile(GBSConstants.GBS_GBS2DB_FILE)
                .taxaFile("/Users/lcj34/Development/tassel5test/dataFiles/CandidateTests/IBMGBSTaxaList.txt")
                .taxaListName("IBM")
                .statFile("outputStats.txt")
                .deleteOldData(true)
                .performFunction(null);

An example of the SNPQualityProfilerPlugin output file can be seen here: SNPQualityProfilerOutput. Note: this is a .txt file that presents better when opened within Excel.