java -Xmx4g -jar /Net/fs1/home/cdurrant/GenomeAnalysisTK-1.5-21/GenomeAnalysisTK.jar -baq CALCULATE_AS_NECESSARY -T UnifiedGenotyper -R ../../wildmice/gatk/NCBIM37_um.fa -o ./raw/snps.raw.chr13.vcf -stand_call_conf 30 -stand_emit_conf 10.0 -I /data/mus/bams/taiwan/tw667_A.bam -I /data/mus/bams/taiwan/tw746_A.bam -I /data/mus/bams/taiwan/tw747_A.bam -I /data/mus/bams/taiwan/tw807_A.bam -I /data/mus/bams/taiwan/tw813_A.bam -I /data/mus/bams/taiwan/tw837_A.bam -I /data/mus/bams/taiwan/tw851_A.bam -I /data/mus/bams/taiwan/tw873_A.bam -I /data/mus/bams/taiwan/tw1000_A.bam -I /data/mus/bams/taiwan/tw1011_A.bam -I /data/mus/bams/taiwan/tw1057_A.bam -I /data/mus/bams/taiwan/tw1143_A.bam -I /data/mus/bams/taiwan/tw1145_A.bam -I /data/mus/bams/taiwan/tw1167_A.bam -I /data/mus/bams/taiwan/tw1172_A.bam -I /data/mus/bams/taiwan/tw1200_A.bam -I /data/mus/bams/taiwan/tw1231_A.bam -I /data/mus/bams/taiwan/tw1237_A.bam -I /data/mus/bams/taiwan/tw1291_A.bam -I /data/mus/bams/taiwan/tw1294_A.bam -L 13 > out13 &