I read that there is a new version of MuTect dealing with indels coming. Would it be possible to know its release date?
We are planning analyses for a new project and would like to know if we can count on MuTect2 or not.
It's a just matter of weeks now, though I can't give you an exact date as we're waiting on the last validation results from collaborators. If you're in the planning phase I think it's probably safe to count on MuTect2 to be out by the time you start processing data.
We have processed our samples with MuTect 1.1.7 and results came out good!
But we have to use another tool for indel detection.
I am wondering how soon we may see the release of MuTect2? Would you add me in the mailing list if there is one? Thanks!
When I called java -jar mutect-1.1.7.jar --version
It said 3.1-0-g72492bb
What kind of version number is this? looks like version 3... not MuTect3...
That's the GATK version number that MuTect 1 is built on top of.
The new MuTect is coming out very soon, we just hit a small technical problem that has delayed the release, but hopefully we'll get it out by the end of the week. (I know I keep saying that but it is the intention).
I believe the new version is out now, I tried running Mutect version 1.1.7 using the standard CL but do not find indels to come up in my vcf file. Can you let me know if there is any additional option to include Indels?
Only MuTect2 calls indels. You can use it in GATK 3.5.
Using MuTect2 for T:N variant calling using the following command
java -Xmx8G -jar GATK-3.5/GenomeAnalysisTK.jar -T MuTect2 -R hs37d5.fa -I:tumor Tumor.bam -I:normal normal.bam --dbsnp dbsnp_138.b37.vcf -nct 2 --cosmicb37_cosmic_v54_120711.vcf -L interval.bed -o Tumor-Normal_MuTect2.vcf
The normal bam is from exome sequenced data. The size of the bams are
MuTect2 has been running for 42.5 hours and only 7.7% of the runs got completed so far. Is there a way to make the runs faster ?
Your best bet is Queue.
Also, have a look at this thread.