Difference between revisions of "GSCAN"
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[https://docs.google.com/document/d/1ZK9VIXxcej3lat_oD_oxPP0ajHwj8yX_FKaPh53svVo/edit# Meeting minutes.] | [https://docs.google.com/document/d/1ZK9VIXxcej3lat_oD_oxPP0ajHwj8yX_FKaPh53svVo/edit# Meeting minutes.] | ||
| + | |||
| + | ==UK Biobank== | ||
| + | <sytaxhighlight lang="bash"> | ||
| + | #!/bin/sh | ||
| + | #SBATCH -A S00000524 | ||
| + | #SBATCH --mem=20gb | ||
| + | #SBATCH --ntasks-per-node=12 | ||
| + | #SBATCH --nodes=1 | ||
| + | #SBATCH --qos janus | ||
| + | #SBATCH --time=0:30:00 | ||
| + | |||
| + | |||
| + | assertNotEmpty() { | ||
| + | : "${!1:? "$1 is empty, aborting."}" | ||
| + | } | ||
| + | |||
| + | |||
| + | # variable | ||
| + | : ${f:=$1} | ||
| + | export f | ||
| + | assertNotEmpty f | ||
| + | |||
| + | vcftools --gzvcf chr20impv1.vcf.gz --positions $f --recode --stdout | bgzip -c > $f.chr20impv1.vcf.gz | ||
| + | </syntaxhighlight> | ||
| + | |||
| + | Then run the command with | ||
| + | |||
| + | <syntaxhighlight lang="bash"> | ||
| + | cat list_of_files_with_position_chunks.txt | parallel sbatch --qos janus --reservation=janus-serial chunk.sh | ||
| + | </syntaxhighlight> | ||
Revision as of 04:48, 18 March 2016
GSCAN GWAS
We track studies in two ways. First, we track analyses with this Google doc. Second, we track study contact info with this Google sheet. These documents are only available to study personnel.
We also track our list of dbGaP studies on this Airtable.
UK Biobank
<sytaxhighlight lang="bash">
- !/bin/sh
- SBATCH -A S00000524
- SBATCH --mem=20gb
- SBATCH --ntasks-per-node=12
- SBATCH --nodes=1
- SBATCH --qos janus
- SBATCH --time=0:30:00
assertNotEmpty() {
: "${!1:? "$1 is empty, aborting."}"
}
- variable
- ${f:=$1}
export f assertNotEmpty f
vcftools --gzvcf chr20impv1.vcf.gz --positions $f --recode --stdout | bgzip -c > $f.chr20impv1.vcf.gz </syntaxhighlight>
Then run the command with
cat list_of_files_with_position_chunks.txt | parallel sbatch --qos janus --reservation=janus-serial chunk.sh