Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Reduce mutect running time
I'm running mutect-1.1.7.jar using java 1.7 on the dutch-lsgrid and it runs longer than the limit imposed of 72 hours wall time as it cannot run in parallel.
How can I reduce the running time by using muTect options? I'm already checking about using a faster CPU.
This is the command line that I'm using:
./jre1.7.0_76/bin/java -Xmx2g -jar mutect-1.1.7.jar -T MuTect -R Homo_sapiens_assembly19.fasta --dbsnp dbsnp_13
2_b37.leftAligned.vcf --cosmic b37_cosmic_v54_120711.vcf --input_file:normal $ATAL_DIR/$NORMALPATH --input_fil
e:tumor $ATAL_DIR/$TUMORPATH --out $MUTECT_OUT
Thanks, Arieh Tal
Dutch Cancer Institute, NKI