Is there any command line commands for LD knni imputation in tassel?

[Mubashir Abbas]

Hello, I am trying to find commands to run LD knni imputation in tassel on linux command line. I searched it in the manual, but there is no pipeline in the manual of Tassel5pipline for command line interface. I can imputate it in GUI  version but my genotype data is very heavy and cannot be imputed there, or either  I have to go for chromosome wise imputation that would be much time consuming. Is there any command to run LD KNNi on linux ?

[Terry Casstevens]

./run_pipeline.pl -Xmx10g -debug -importGuess mdp_genotype.hmp.txt
-LDKNNiImputationPlugin -endPlugin -export LDKNNOutput


https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/Tassel_Pipeline_Tutorial20160330.pdf

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/Tassel5PipelineCLI.pdf


./run_pipeline.pl -LDKNNiImputationPlugin -help

./lib/jhdf5-14.12.5.jar:./lib/kotlinx-coroutines-core-1.3.0.jar:./lib/htsjdk-2.19.0.jar:./lib/scala-library-2.10.1.jar:./lib/javax.json-1.0.4.jar:./lib/kotlin-stdlib-jdk8-1.3.50.jar:./lib/junit-4.10.jar:./lib/gs-ui-1.3.jar:./lib/guava-22.0.jar:./lib/ejml-0.23.jar:./lib/kotlin-stdlib-1.3.50.jar:./lib/ahocorasick-0.2.4.jar:./lib/forester-1.038.jar:./lib/jfreechart-1.0.19.jar:./lib/log4j-1.2.13.jar:./lib/colt-1.2.0.jar:./lib/kotlin-stdlib-jdk7-1.3.50.jar:./lib/biojava-alignment-4.0.0.jar:./lib/json-simple-1.1.1.jar:./lib/commons-math3-3.4.1.jar:./lib/snappy-java-1.1.1.6.jar:./lib/mail-1.4.jar:./lib/commons-codec-1.10.jar:./lib/biojava-phylo-4.0.0.jar:./lib/jfreesvg-3.2.jar:./lib/itextpdf-5.1.0.jar:./lib/slf4j-simple-1.7.10.jar:./lib/gs-core-1.3.jar:./lib/biojava-core-4.0.0.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/jcommon-1.0.23.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/fastutil-8.2.2.jar:./lib/slf4j-api-1.7.10.jar:./lib/phg.jar:./lib/trove-3.0.3.jar:./sTASSEL.jar

Memory Settings: -Xms512m -Xmx1536m

Tassel Pipeline Arguments: -LDKNNiImputationPlugin -help

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version:
5.2.67 Date: November 10, 2020

[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_202

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

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16

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

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

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

Usage:

LDKNNiImputationPlugin <options>

-highLDSSites <High LD Sites> : Number of sites in high LD to use in
imputation [2..2000] (Default: 30)

-knnTaxa <Number of nearest neighbors> : Number of neighbors to use in
imputation [2..200] (Default: 10)

-maxLDDistance <Max distance between site to find LD> : Maximum
physical distance between sites to search for LD (-1 for no distance
cutoff - unlinked chromosomes will be tested) (Default: 10000000)

On Thu, Nov 12, 2020 at 8:18 AM Mubashir Abbas
<mubashir...@gmail.com> wrote:
>
> Hello, I am trying to find commands to run LD knni imputation in tassel on linux command line. I searched it in the manual, but there is no pipeline in the manual of Tassel5pipline for command line interface. I can imputate it in GUI version but my genotype data is very heavy and cannot be imputed there, or either I have to go for chromosome wise imputation that would be much time consuming. Is there any command to run LD KNNi on linux ?
>

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[Mubashir Abbas]

Highly appreciated, Thank you so much for very quick response. Best regards.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CACHsrTsLqDzbfUBY_7BY0y4ft1dr7MmoGCcrnEgn6ThLhqsWCg%40mail.gmail.com.