homework_7_functional_annotation
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homework_7_functional_annotation [2015/12/02 15:44] scott |
homework_7_functional_annotation [2015/12/03 14:22] (current) scott /* Code for Homework */ |
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| ==== Notes ==== | ==== Notes ==== | ||
| - | * BioFrontiers system admins have not installed ANNO just yet. Should be ready by class time tomorrow (12/3).* | ||
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| # Some modules you'll need | # Some modules you'll need | ||
| module load tabix_0.2.6 | module load tabix_0.2.6 | ||
| - | module load anno | + | module load anno_1.0 |
| - | module load plink_latest | + | |
| # I encourage you to annotate your own genome, but for purposes of this | # I encourage you to annotate your own genome, but for purposes of this | ||
| Line 40: | Line 38: | ||
| -o chrALL.filtered.PASS.beagled.HG00096.rsID.anno.vcf.gz \ | -o chrALL.filtered.PASS.beagled.HG00096.rsID.anno.vcf.gz \ | ||
| -r / | -r / | ||
| - | -g / | + | -g / |
| -p / | -p / | ||
| -c / | -c / | ||
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| ### The following command tells me at how many sites this individual | ### The following command tells me at how many sites this individual | ||
| ### has a heterozygous stop gain allele: | ### has a heterozygous stop gain allele: | ||
| - | zgrep ' | + | zgrep ' |
| ### | ### | ||
homework_7_functional_annotation.1449096251.txt.gz · Last modified: 2015/12/02 15:44 by scott
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