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The $GCOUT/split/chr20 folder contains a VCF with just the sites that pass the filters.
The $GCOUT/split/chr20 folder contains a VCF with just the sites that pass the filters.
ls $GCOUT/split/chr20/
* '''chr20.filtered.PASS.vcf.gz ''' – vcf of just sites that pass all filters
* '''chr20.filtered.PASS.vcf.gz ''' – vcf of just sites that pass all filters
* chr20.filtered.PASS.split.1.vcf.gz - intermediate file
* chr20.filtered.PASS.split.1.vcf.gz - intermediate file
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 GotCloud Genotype Refinement Pipeline ==
