Post date: Sep 17, 2013 9:17:5 PM
I am using samtools mpileup to generate a bcf file for variant calling. The results will be in projects/timema_wgwild/. I am running this with (1.3 in outfile name) and without the -6 option, which assumes Illumina 1.3+ encoding. I think the oxford data uses sanger encoding and that this option is not needed, but I want to see how much of a difference it makes. Here is the exact command (in the jobsub.sh script) without the -6 option:
samtools mpileup -P ILLUMINA -u -g -I -f ../lg_timemaGenome.fasta timema[LMPRH]*sorted.bam > /home/A01963476/projects/timema_wgwild/wildwg.bcf
The jobs are queued (id 14557 and 14558).