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, 16:21, 4 March 2013
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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/ | + | 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 |
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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. |
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| == STEP 4 : Run GotCloud Genotype Refinement Pipeline == | | == STEP 4 : Run GotCloud Genotype Refinement Pipeline == |