Test-drive the GATK tools and Best Practices pipelines on Terra
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Mutect2 takes too mach time？
I've been calling somatic mutations with Mutect2 on WES data, and have noted that the time Mutect2 takes were too long.Like below(sorry for I can not upload pictures)
INFO 15:10:32,095 ProgressMeter - | processed | time | per 1M | | total | remaining
21 INFO 15:10:32,096 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
24139 INFO 10:08:19,413 ProgressMeter - chr21:47664676 2.60987991203E11 16.8 d 5.0 s 94.0% 17.9 d 25.9 h
24140 INFO 10:09:19,433 ProgressMeter - chr21:47693250 2.60995921308E11 16.8 d 5.0 s 94.0% 17.9 d 25.9 h
24141 INFO 10:10:19,455 ProgressMeter - chr21:47700345 2.60998197418E11 16.8 d 5.0 s 94.0% 17.9 d 25.9 h
24142 INFO 10:11:19,475 ProgressMeter - chr21:47703946 2.60998767018E11 16.8 d 5.0 s 94.0% 17.9 d 25.9 h
24143 INFO 10:12:19,495 ProgressMeter - chr21:47704320 2.60998767018E11 16.8 d 5.0 s 94.0% 17.9 d 25.9 h
Is this normal ? Am I missing something/misinterpreting?
-T MuTect2 -R reference.fa -I:normal normal.bam -I:tumor tumor.bam --dbsnp dbsnp.vcf.gz --cosmic cosmic_v74.vcf.gz -L target.intervals -o result.vcf
Any comments and help greatly appreciated!