Command line filtering for loci based upon file

[danj...@gmail.com]

Greetings,

I have a number of files specifying different locus filtering strategies and would like to apply them to a genotype table from the command line. I can do this easily from the GUI by going to the Filter -> Filter Genotype Table Sites -> Position List and uploading my JSON file of the loci that I would like to extract but I haven't been able to find the command to do this from the command line. I've tried out the different filter commands and they aren't getting me to where I need to be. Am I missing something simple?

Thanks for your help!

-Dan

[Terry Casstevens]

FilterSiteBuilderPlugin -positionList positions.json -endPlugin


./run_pipeline.pl -FilterSiteBuilderPlugin -help

./lib/ahocorasick-0.2.4.jar:./lib/avro-1.8.1.jar:./lib/biojava-alignment-4.0.0.jar:./lib/biojava-core-4.0.0.jar:./lib/biojava-phylo-4.0.0.jar:./lib/colt-1.2.0.jar:./lib/commons-codec-1.10.jar:./lib/commons-math3-3.4.1.jar:./lib/ejml-0.23.jar:./lib/forester-1.038.jar:./lib/guava-22.0.jar:./lib/htsjdk-2.11.0.jar:./lib/itextpdf-5.1.0.jar:./lib/javax.json-1.0.4.jar:./lib/jcommon-1.0.23.jar:./lib/je-6.0.11.jar:./lib/jfreechart-1.0.19.jar:./lib/jfreesvg-3.2.jar:./lib/jfxrt.jar:./lib/jhdf5-14.12.5.jar:./lib/json-simple-1.1.1.jar:./lib/junit-4.10.jar:./lib/log4j-1.2.13.jar:./lib/mail-1.4.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/slf4j-api-1.7.10.jar:./lib/slf4j-simple-1.7.10.jar:./lib/snappy-java-1.1.1.6.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/trove-3.0.3.jar:./dist/sTASSEL.jar

Memory Settings: -Xms512m -Xmx1536m

Tassel Pipeline Arguments: -FilterSiteBuilderPlugin -help

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version:
5.2.38 Date: July 13, 2017

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available
Memory Reported by JVM: 1365 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_121

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel
Pipeline Arguments: [-fork1, -FilterSiteBuilderPlugin, -help,
-runfork1]

[main] ERROR net.maizegenetics.plugindef.AbstractPlugin - Unrecognized
argument: -help

[main] INFO net.maizegenetics.plugindef.AbstractPlugin -

Usage:

FilterSiteBuilderPlugin <options>

-filterName <Filter Name> : Filter Name (Default: Filter)

-siteMinCount <Site Min Count> : Site Minimum Count of Alleles not
Unknown [0..+∞) (Default: 0)

-siteMinAlleleFreq <Site Min Allele Freq> : Site Minimum Minor Allele
Frequency [0.0..1.0] (Default: 0.0)

-siteMaxAlleleFreq <Site Max Allele Freq> : Site Maximum Minor Allele
Frequency [0.0..1.0] (Default: 1.0)

-minHeterozygous <Min Heterozygous Proportion> : Min Heterozygous
Proportion [0.0..1.0] (Default: 0.0)

-maxHeterozygous <Max Heterozygous Proportion> : Max Heterozygous
Proportion [0.0..1.0] (Default: 1.0)

-removeMinorSNPStates <true | false> : Remove Minor SNP States (Default: false)

-siteRangeFilterType <Site Range Filter Type> : True if filtering by
site numbers. False if filtering by chromosome and position [NONE,
SITES, POSITIONS] (Default: NONE)

-startSite <Start Site> : Start Site [0..+∞) (Default: 0)

-endSite <End Site> : End Site [0..+∞) (Default: 0)

-startChr <Start Chr> : Start Chr

-startPos <Start Pos> : Start Pos [0..+∞)

-endChr <End Chr> : End Chr

-endPos <End Pos> : End Pos [0..+∞)

-includeSites <true | false> : Include Sites (Default: true)

-positionList <Position List> : Filter based on position list.

-siteNames <Site Names> : Filter based on site names.

-bedFile <Bed File> : Filter based on BED file.

-chrPosFile <Chr Pos File> : Filter based on list of chromsome /
position in file.

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