Updated 2021-02-10

Samtools pbs

#PBS -N samtoolsTest
#PBS -A [Account]
#PBS -l nodes=1:ppn=2
#PBS -l pmem=8gb
#PBS -l walltime=10:00
#PBS -q inferno
#PBS -j oe
#PBS -o samtoolsTest.out

cd $PBS_O_WORKDIR
module load samtools

# Convert SAM to its binary counterpart, BAM
samtools view -S -b sample.sam > sample.bam