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Line 227: − == STEP 5 : Run Support Vector Machine (SVM) Pipeline ==
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Note: the tutorial does not produce a target directory, but if you run with targeted data, you may see that.
Note: the tutorial does not produce a target directory, but if you run with targeted data, you may see that.
== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==
== STEP 4 : Run Support Vector Machine (SVM) Pipeline ==
== STEP 5 : Run GotCloud Genotype Refinement Pipeline ==
The next step is to perform genotype refinement using linkage disequilibrium information using [http://faculty.washington.edu/browning/beagle/beagle.html Beagle] & [[ThunderVCF]].
The next step is to perform genotype refinement using linkage disequilibrium information using [http://faculty.washington.edu/browning/beagle/beagle.html Beagle] & [[ThunderVCF]].
ls $GCOUT/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz $GCOUT/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi
ls $GCOUT/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz $GCOUT/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi
