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--- guides:slurm:basics [16.10.2020 10:47]
Juha Kekäläinen
+++ guides:slurm:basics [27.11.2023 12:40] (current)
Administrator
@@ Line 35: / Line 35: @@
 #SBATCH --mem=2000		# Reserve 2 GB RAM for the job
 #SBATCH --partition serial	# Partition to submit
-module load matlab/R2018b # load modules
+module load matlab/R2022b # load modules
 matlab -nodisplay < matlab.m # Execute the script
@@ Line 47: / Line 48: @@
 ```
 **[sbatch](https://slurm.schedmd.com/sbatch.html)** command submits the job to the job queue and executes the **[bash script](https://en.wikipedia.org/wiki/Bash_(Unix_shell)**.
+Here is an another example on how to analyze variants.
+```
+#!/bin/bash
+#SBATCH --ntasks 1          # Number of task
+#SBATCH --time 00:30:00     # Runtime 30min
+#SBATCH --mem 2000          # Reserve 2 GB RAM for the job
+#SBATCH --partition serial  # Partition to submit
+module load bcftools # load modules
+# filter variants and calculate stats
+bcftools filter --include'%QUAL>20' calls.vcf.gz | bcftools stats --output calls_filtered.stats
+```
+Submit the job to computing queue with the **[sbatch](https://slurm.schedmd.com/sbatch.html)** command.
+```
+sbatch variants.sbatch
+```
@@ Line 83: / Line 105: @@
 ```
 scontrol show job <jobid>
-```
-#### Extend runtime of given jobid
-```
-scontrol update jobid=<job_id> TimeLimit=<new_timelimit>
 ```

Bioinformatics Center