Question: Can a normal tissue sequence be used for various tumor samples in Varscan Somatic or GATK MuTect2?
1
gravatar for tarekzakaria.badr
9 weeks ago by
tarekzakaria.badr30 wrote:

I have exome sequencing data from tumor samples from mice with only one of them has tumor/normal tissue sequence. All the mice share the same genetic background, bred together and i believe they come from the same mother (not 100% sure about the same mother though). I have aligned them sequences using BWA-mem, marked the duplicates, etc.., and now want to call the variants either using VarScan somatic or GATK MuTect2. Is it possible to use this normal tissue sequence as a common Normal tissue for the other tumor sequences from the other mice? or is it better to call the tumors and the normal sequences individually then filter the Germline Variants afterwards from the Tumor samples?

Thanks in advance

mutect2 varscan gatk • 162 views
ADD COMMENTlink modified 8 weeks ago by Charles Warden6.5k • written 9 weeks ago by tarekzakaria.badr30
1

Only 1 sample for normal is very little!

However, wherever possible, run T/N pairs , rather than running each of them individually. Normals are there not only to filter the somatic mutations, but also to minimize the technical biases.

https://software.broadinstitute.org/gatk/documentation/article?id=11053

https://gatkforums.broadinstitute.org/gatk/discussion/4462/what-input-files-does-mutect-accept-require

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Santosh Anand4.7k

Thanks for your reply. I know it's very little but unfortunately i received the sequences after they have ended the experiments. Following your advice I will then run this normal tissue with the other tumor samples as a Normal/Tumor pair. I also have found SNPS and indels VCF files for mm10 and will try to filter through these also.

ADD REPLYlink written 9 weeks ago by tarekzakaria.badr30

Sounds good. Keep in mind that mm8 is a consensus genome, which might be different from the genome of strain of your mice. You could check VCFs of other strains here

https://www.sanger.ac.uk/science/data/mouse-genomes-project

ADD REPLYlink written 9 weeks ago by Santosh Anand4.7k
1
gravatar for Charles Warden
8 weeks ago by
Charles Warden6.5k
Duarte, CA
Charles Warden6.5k wrote:

Perhaps you could try GATK joint variant calls (among your tumor samples)?

While not exactly designed for somatic variant calling, it should increase your sensitivity and help you find recurrent tumor variants.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Charles Warden6.5k
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