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Running time of unifiedgenotyper
Hi, I'm using unifiedgenotyper for the SNP calling in one lane illumina RNA-seq data, the bam file is ~15gb. The command I used is:
java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R assembly.fa -I seq.bam --out result.vcf -ploidy 48 -stand_call_conf 20 -stand_emit_conf 20.0
I run it with 2 cpus and 72gb memory. It has been run for 3 days (I also used -nt 12 to run it with 12 cpus at the same time but the speed didn't improve significantly) and haven't finished. In addition, there are only 6000 loci were write into the vcf file by now, but I analysed this data using other pipelines at the same time, all of them have been finished and reported ~1 million loci.
So can anybody tell me usually how long it will take for unifiedgenotyper to analysis one lane illumina RNA-seq data? Thanks.