GATK to BEAGLE interface

stechenstechen University of PennsylvaniaPosts: 23Member


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 like=beagle_input_410_impute phased=~/stechen/phase_ref/ALL.chr1.phase1_release_v3.20101123.filt.bgl markers=~stechen/phase_ref/ALL.chr1.phase1_release_v3.20101123.filt.markers missing=? out=beagle_output_410_chr1

[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: -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)


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