Filtering indels

[jlblanc...@gmail.com]

Hi I am trying to filter out the snps from my dataset following this command line:

/usr/local/bin/tassel-5-standalone/run_pipeline.pl -Xmx400G -fork1 -h5 /nobackup/data7/jose/GBSv2/MedicagoGenotypes_KO.h5 -filterAlign -filterAlignExtInd -export /nobackup/data7/jose/GBSv2/MedicagoGenotypes_KO_NoIndels.h5 -runfork1 | tee GBSv2logfile.txt

But got this error:

java.lang.UnsupportedOperationException

        at net.maizegenetics.analysis.filter.FilterAlignmentPlugin.processDatum(FilterAlignmentPlugin.java:190)

        at net.maizegenetics.analysis.filter.FilterAlignmentPlugin.performFunction(FilterAlignmentPlugin.java:82)

        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1490)

        at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1397)

        at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:216)

        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1490)

        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

        at java.util.concurrent.FutureTask.run(FutureTask.java:266)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

        at java.lang.Thread.run(Thread.java:745)

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Aug 28, 2015 13:37:44: progress: 100%

Any idea of what is wrong?

Thanks

José

[Terry Casstevens]

The flag -filterAlignExtInd means to extract indels but it hasn't been
implemented. What kind of filtering are trying to do?

Best,

Terry

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[José Luis Blanco Pastor]

Precisely, I was trying to extract indels. It seems that I have managed to do it with the GUI version of TASSEL with Impute/Remove indels for imput to Beagle v.4

Cheers
José

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[Terry Casstevens]

That feature existed in an earlier version of Tassel but hasn't yet
migrated to Tassel 5. I'll need to talk with my colleagues about
that.

What are you thinking this function should do?

Best,

Terry

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[José Luis Blanco Pastor]

I think it should eliminate loci containing gaps "0/-" in any of the samples. I really think that "Impute/Remove indels for imput to Beagle v.4" did the job as I could observe in the output file.

Cheers,
José.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CACHsrTujQ6Rq0tORVHLOkPPO260tTuCKC789qqh7GxmF1a0z4w%40mail.gmail.com.

[Edward S. Buckler]

Yes, Terry - I think site filtering in normal TASSEL 5 should provide a indel filtering option.

Cheers-
Ed

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[José Luis Blanco Pastor]

I have just realized that "Impute/Remove indels for imput to Beagle v.4" in normal TASSEL 5 gives an invalid vcf formatted file with lots of missing information.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/2E7FFA3D-CFB6-484E-97FA-D5E202CAAE01%40cornell.edu.

[lfsa...@ncsu.edu]

Hello,
I'm trying to filter out indels (A/-/T, T/-/G, etc.) by running the following code but I do not get any successful results (below is the console output).

run_pipeline.bat -Xms5g -Xmx50g -fork1 -h D:\LFSL\235maize_diversity_10.hmp.txt -filterAlign -filterAlignExtInd -export D:\LFSL\Geno\235maize_diversity_10_fil2

Any suggestion?

Thank you in advance

Luis

C:\Program Files\TASSEL5>run_pipeline.bat -Xms5g -Xmx50g -fork1 -h D:\LFSL\235ma
ize_diversity_10.hmp.txt -filterAlign -filterAlignExtInd -export D:\LFSL\Geno\23
5maize_diversity_10_fil2
.\sTASSEL.jar;.\lib\ahocorasick-0.2.4.jar;.\lib\batik-awt-util.jar;.\lib\batik-c
ss.jar;.\lib\batik-dom.jar;.\lib\batik-ext.jar;.\lib\batik-gui-util.jar;.\lib\ba
tik-gvt.jar;.\lib\batik-parser.jar;.\lib\batik-svg-dom.jar;.\lib\batik-svggen.ja
r;.\lib\batik-util.jar;.\lib\batik-xml.jar;.\lib\biojava-alignment-4.0.0.jar;.\l
ib\biojava-core-4.0.0.jar;.\lib\biojava-phylo-4.0.0.jar;.\lib\cisd-jhdf5-batteri
es_included_lin_win_mac.jar;.\lib\colt.jar;.\lib\commons-codec-1.10.jar;.\lib\co
mmons-math3-3.4.1.jar;.\lib\ejml-0.23.jar;.\lib\forester.jar;.\lib\geronimo-spec
-activation-1.0.2-rc4.jar;.\lib\guava-14.0.1.jar;.\lib\htsjdk-1.138.jar;.\lib\it
extpdf-5.1.0.jar;.\lib\javax.json-1.0.4.jar;.\lib\jcommon-1.0.6.jar;.\lib\jfreec
hart-1.0.3.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\poi-3.0.1-FINAL-20070705.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\sTASSEL.jar;.\li
b\trove-3.0.3.jar;.\lib\xercesImpl.jar;.\lib\xml.jar;.\lib\xmlParserAPIs.jar
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.24  Dat
e: April 7, 2016
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Report
ed by JVM: 45511 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_91
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Windows 7
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Argument
s: [-fork1, -h, D:\LFSL\235maize_diversity_10.hmp.txt, -filterAlign, -filterAlig
nExtInd, -export, D:\LFSL\Geno\235maize_diversity_10_fil2]
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Lo
ading File: D:\LFSL\235maize_diversity_10.hmp.txt time: Apr 25, 2016 8:13:59
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegene
tics.analysis.data.FileLoadPlugin: time: Apr 25, 2016 8:14:0: progress: 33%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegene
tics.analysis.data.FileLoadPlugin: time: Apr 25, 2016 8:14:0: progress: 66%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegene
tics.analysis.data.FileLoadPlugin: time: Apr 25, 2016 8:14:0: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegen
etics.analysis.data.FileLoadPlugin  Citation: Bradbury PJ, Zhang Z, Kroon DE, Ca
sstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapp
ing of complex traits in diverse samples. Bioinformatics 23:2633-2635.
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished
 Loading File: D:\LFSL\235maize_diversity_10.hmp.txt time: Apr 25, 2016 8:14:0
Genotype Table Name: 235maize_diversity_10
Number of Taxa: 235
Number of Sites: 66589
Sites x Taxa: 15648415
Chromosomes...
10: start site: 0 (2918) last site: 66588 (149584901) total: 66589

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegene
tics.analysis.filter.FilterAlignmentPlugin: time: Apr 25, 2016 8:14:1: progress:
 100%
java.lang.UnsupportedOperationException
        at net.maizegenetics.analysis.filter.FilterAlignmentPlugin.processDatum(
FilterAlignmentPlugin.java:190)
        at net.maizegenetics.analysis.filter.FilterAlignmentPlugin.performFuncti
on(FilterAlignmentPlugin.java:82)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPl
ugin.java:1631)
        at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(Abstra
ctPlugin.java:1538)
        at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLo
adPlugin.java:274)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPl
ugin.java:1631)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPlugin
Listener.java:29)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegene
tics.analysis.data.FileLoadPlugin: time: Apr 25, 2016 8:14:1: progress: 100%