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GotCloud: FAQs

921 bytes added, 10:54, 23 June 2015
Variant Calling Pipeline FAQs
::#* gotcloud/bin/genomestrip.pl - you only need to update this one if you want to run genomestrip
::#* gotcloud/scripts/bed-diff.pl - you only need to update this one if you plan to run bed-diff.pl
 
 
== ldrefine Pipeline FAQs ==
; make<nowiki>: *** [outdir/beagle/chr#/split/bgl.#.chr#.PASS.#.vcf.gz.tbi] Error 1</nowiki>
: Check the log file at: <code>outdir/beagle/chr#/split/bgl.#.err</code>
: If it says:
:: '''Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -2'''
::: '''at phaser.j.a(Unknown Source)<br /> at phaser.j.c(Unknown Source)<br /> at phaser.h.a(Unknown Source)<br /> at phaser.E.a(Unknown Source)<br /> at phaser.Y.a(Unknown Source)<br /> at phaser.PhaseMain.<init>(Unknown Source)<br /> at phaser.PhaseMain.main(Unknown Source)'''
: You need to change the seed for running beagle.
:* In your configuration file, set:
:** <code>BEAGLE = java -Xmx4g -jar $(BIN_DIR)/beagle.20101226.jar seed=993470 gprobs=true niterations=50 lowmem=true</code>
:* If it fails again, change the seed in the above command to something else, and rerun.
== Tutorial FAQs ==

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