Post date: Aug 08, 2014 10:58:22 PM
I am calling variants and calculating genotype likelihoods with GATK's UnifiedGenotyper. I might use these for base quality recalibration or just take these as the calls depending on how long this take. These will be hight quality variants anyway, as I am using a phred-scaled confidence of 50 (rather than 30). Here is the submission script:
#!/bin/sh
#PBS -N pbs.zgompert
#PBS -l nodes=1:ppn=32
#PBS -l walltime=96:00:00
#PBS -l mem=960g
#PBS -q batch
. /rc/tools/utils/dkinit
reuse GATK
cd /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/
java -jar -Xmx900g /rc/tools/free/redhat_6_x86_64/gatk-3.1.1/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /labs/evolution/data/timema/draft_genome/draft0.3/mod_lg_timemaGenome.fasta -I bams.list -o variants.vcf -nt 32 -glm SNP -hets 0.001 -mbq 20 -ploidy 2 -stand_call_conf 50 -maxAltAlleles 2
Note, this is using 32 cores and requesting 960 gb total RAM.