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support:hpc:software:samtools

SamTools

SamTools SamTools stands for Sequence Alignment/Map

To load SamTools type the following:

$ module load gcc samtools

SAMtools is installed on farm.caes.ucdavis.edu under /share/apps/samtools-0.1.18

Submitting a single SAMtools batch job

Put the sample files under your home directory:

mkdir ~/samtools/run1; cd ~/samtools/run1 ; cp /share/apps/samtools-0.1.18/gcc/4.5/examples/ex1.* .; tar xvfz ex1.sam.gz

3. Create a script file. The file will contain the lines similar to the lines below. Modify the path of location before running.

#!/bin/bash
# This file is runSamtools
#
# following option makes sure the job will run in the current directory
#$ -cwd
module load gcc samtools
cd ~/samtools/run1
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
samtools index ex1.bam
samtools tview ex1.bam ex1.fa
samtools pileup -cf ex1.fa ex1.bam

4. Submit the script using the 'qsub' command on farm.caes.ucdavis.edu.

qsub ~username/runSamtools

Manual

support/hpc/software/samtools.txt · Last modified: 2012/02/07 14:30 by tlknight