Question: Mutect 2 on WGS data takes too long to run
0
gravatar for DVA
2.8 years ago by
DVA540
United States
DVA540 wrote:

I used Mutect2 on human exome sequencing (30x) data before and without parallel processing, it took me 5.5 days. That was still doable - However, now I am trying to run Mutect2 on my human WGS data (30x, bqsr bam file size ~120G), the estimation tells me 500+ weeks at the start!

I feel like even I split on regions, or use Queue offered by GATK will not improve the situation to a satisfying level... Here is my code:

java -jar $GATK -T MuTect2 -R $REF -I:tumor $BQSRTBam -I:normal $BQSRNBam --dbsnp $DBSNP --cosmic $cosmicData -o $mutect2VCF

I tried different memory, and with/without dbsnp/cosmic... going without cosmic seems to let Mutect2 give a longer estimation.

Anyone experience similar issues? Any suggestion is appreciated. Thank you very much in advance.

mutect wgs • 1.9k views
ADD COMMENTlink modified 2.8 years ago by donfreed1.5k • written 2.8 years ago by DVA540
1
gravatar for chen
2.8 years ago by
chen2.0k
OpenGene
chen2.0k wrote:

Varscan2 instead is another choice, much faster.

ADD COMMENTlink written 2.8 years ago by chen2.0k

I had a little experience with VarScan2 - don't you need to use samtools pileup? I recall the pileup procedure to be painfully long too... Maybe I did not do it correctly, but please comment on it. Thank you.

ADD REPLYlink written 2.8 years ago by DVA540
1

Yes, you are right, samtools mipileup is needed. But samtools mpileup + VarScan2 is still much much faster than MuTect2.

ADD REPLYlink written 2.8 years ago by chen2.0k
1
gravatar for donfreed
2.8 years ago by
donfreed1.5k
Mountain View, CA
donfreed1.5k wrote:

You can try the Sentieon Genomic Tools: http://www.biorxiv.org/content/early/2017/05/12/115717. We provide a variant caller (TNhaplotyper, part of TNseq) that provides matching results to MuTect2 with a substantial performance improvement. You can request a free trial from https://www.sentieon.com/home/free-trial/.

ADD COMMENTlink written 2.8 years ago by donfreed1.5k
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