Post date: Oct 02, 2014 3:17:14 PM
I am calling variants with GATK using the *unique.bam files. I am running one LG at a time with the following commands (in job_var1.sh):
. /rc/tools/utils/dkinit
reuse GATK
cd /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/
java -jar -Xmx900g -Djava.io.tmpdir=/pscratch/A01963476/ /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 -L lg2intervals.list -o variantsLG2.vcf -nt 48 -glm SNP -hets 0.001 -mbq 20 -ploidy 2 -stand_call_conf 50 -maxAltAlleles 2
The initial results will be in /labs/evolution/data/timema/timema_wgrs/assembliesExperiment but I will move them to projects later.