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I'm trying to phase GATK genotype and to impute some SNP calls. Before I could do that, I must convert GATK results to an acceptable BEAGLE input format. What's the difference between VariantsToBeagleUnphased and ProduceBeagleInput? I know the latter outputs a file with genotype likelihoods. Incidentally, using that file didn't work in BEAGLE and produced the following log and error files. Can anyone give any pointers? Thanks in advance!
[stechen@node24 ~]$ more beagle_run_410.o720239
Beagle version 3.3.2 (31 Oct 2011)
Enter "java -jar beagle.jar" for summary of command line arguments.
Start time: 11:59 AM EDT on 07 Aug 2013
Command line: java -Xmx7281m -jar beagle.jar
[stechen@node24 ~]$ more beagle_run_410.e720239
bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=~stechen/tmp -Xms256m -Xmx8G
Exception in thread "main" java.lang.NullPointerException
at phaser.y.a(Unknown Source)
at phaser.y.(Unknown Source)
at phaser.H.a(Unknown Source)
at phaser.v.(Unknown Source)
at phaser.PhaseMain.(Unknown Source)
at phaser.PhaseMain.main(Unknown Source)