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Genotype Refinement Input
=== Genotype Refinement Input ===
The GotCloud genotype refinement pipeline takes as input ${OUT}/split/chr22/chr22.filtered.PASS.vcf.gz (the VCF file of PASS'ing SNPs from snpcall as input.
The bam index and the configuration file we used for GotCloud snpcall will tell GotCloud genotype refinement everything it needs to know, so no new input files need to be prepared.
 
Note: the configuration file overrides the THUNDER command to make it go faster than the default settings so the tutorial will run faster:
[[File:thunderConf.png|600px]]
=== Running GotCloud Genotype Refinement ===

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