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, 09:23, 22 May 2015Reverted edits by Hmkang (talk) to last revision by Mktrost
== Friday ==
== Friday ==
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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]]
=== Association Analysis Tutorial ===
Now we are going to run the Association Analysis Practical
Please go to: [[SeqShop: Association Analysis, May 2015]]
We will look at our own genomes again after the practical.
=== Return to SeqShop: Ancestry On Your Own Genome, May 2015 ===
=== Return to SeqShop: Ancestry On Your Own Genome, May 2015 ===
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
export HK=/home/hmkang/apigenome/bin/
export HK=/net/seqshop-server/home/hmkang/seqshop/bin
==== Annotation / Lookup against dbSNP ====
==== Annotation / Lookup against dbSNP ====
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
$HK/run-make --cmd "$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
Looking up SNPs by rsID is possible by (for example)
Looking up SNPs by rsID is possible by (for example)
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
==== Extracting only exonic SNPs ====
==== Extracting only exonic SNPs ====
