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, 09:23, 22 May 2015
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| == Friday == | | == Friday == |
− | <div class="mw-collapsible"> | + | <div class="mw-collapsible-content mw-collapsed"> |
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| === SeqShop: Ancestry On Your Own Genome, May 2015 === | | === SeqShop: Ancestry On Your Own Genome, May 2015 === |
| [[SeqShop: Ancestry On Your Own Genome, May 2015]] | | [[SeqShop: Ancestry On Your Own Genome, May 2015]] |
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| + | === Association Analysis Tutorial === |
| + | Now we are going to run the Association Analysis Practical |
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| + | Please go to: [[SeqShop: Association Analysis, May 2015]] |
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| + | We will look at our own genomes again after the practical. |
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| === Return to SeqShop: Ancestry On Your Own Genome, May 2015 === | | === Return to SeqShop: Ancestry On Your Own Genome, May 2015 === |
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| In addition, set another environmental variable for locating the binaries for custom analysis | | In addition, set another environmental variable for locating the binaries for custom analysis |
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− | export HK=/home/hmkang/apigenome/bin/ | + | export HK=/net/seqshop-server/home/hmkang/seqshop/bin |
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| ==== Annotation / Lookup against dbSNP ==== | | ==== Annotation / Lookup against dbSNP ==== |
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| If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs | | If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs |
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− | $HK/run-make --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbSNP.b138/dbsnp_138.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --repeat-chr --numjobs 6 | + | $HK/run-command-wgs --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbSNP.b138/dbsnp_138.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --numjobs 6 |
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| Looking up SNPs by rsID is possible by (for example) | | Looking up SNPs by rsID is possible by (for example) |
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| Or you can run multiple chromosomes in parallel in one command | | Or you can run multiple chromosomes in parallel in one command |
− | $HK/run-make --cmd "$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz" --repeat-chr --numjobs 6 | + | $HK/run-command-wgs --cmd "$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz" --numjobs 6 |
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| ==== Extracting only exonic SNPs ==== | | ==== Extracting only exonic SNPs ==== |