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homework_7_functional_annotation [2015/12/02 15:51] scott /* Code for Homework */ |
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 |
# 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 | ||
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-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 ' |
### | ### |