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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