SNPCutPosTagVerificationPlugin allows a user to specify a Cut or SNP position for which they would like data printed. For a cut position, the tags associated with that position are printed along with the number of times it appears in each taxa.

For a SNP position, each allele and the tags associated with that allele are printed along with the number of time the tag appears in each taxa. The tag is shown both as it is stored in the database and as a forward strand. The SNP alignments are based on the forward strand.

The parameters to this plugin are:

• -db< Input Database> : Input database file (REQUIRED)
• -chr <Chromosome> : Chromosome containing the position. (REQUIRED)
• -pos < Position> : A cut or SNP position number. (REQUIRED)
• -strand <Strand> : The strand direction: 0=reverse, 1=forward (REQUIRED)
• -type < cut/snp> : The type of position, either cut or snp, for which the taxa distribution will be presented.
• -outFile <Output file> : File name to which tab delimited output will be written.

To run this command from the command line:

#!java

./run_pipeline.pl -fork1 -SNPCutPosTagVerificationPlugin
-db /Users/lcj34/git/tassel-5-test/tempDir/GBS/Chr9_10-20000000/GBSv2.db -chr 9 
-pos 187567 -strand 1 -type snp -outFile /Users/lcj34/myOutFile
-endPlugin -runfork1

To call the UpdateSNPPositionQualityPlugin from program code:

#!java

                new SNPCutPosTagVerificationPlugin()
                .gBSDBFile(GBSConstants.GBS_GBS2DB_FILE)
                .chrom("9")
                .strand((byte)1)
                .cutOrSnpPosition(187567)
                .positionType("snp")
                .outFile(myOutFile)
                .performFunction(null);