GSCAN

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.

Meeting minutes.

UK Biobank

<sytaxhighlight lang="bash">

1. !/bin/sh
2. SBATCH -A S00000524
3. SBATCH --mem=20gb
4. SBATCH --ntasks-per-node=12
5. SBATCH --nodes=1
6. SBATCH --qos janus
7. SBATCH --time=0:30:00

assertNotEmpty() {

   : "${!1:? "$1 is empty, aborting."}"

}

1. 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