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Old 05-31-2012, 11:56 AM   #1
NGSNewbie1
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Default Tumor/Normal comparison tool for VCF?

Sorry for this newbie question but I haven't been able to get an answer after searching around. Is there a program that automagically produces the somatic mutations from inputted tumor and normal VCF files? I'm trying to avoid using a tool like SomaticSniper with BAM files because of size/computation etc. If I have the VCF files, is there an easy way to just select the differences?

Thank you in advance for any guidance!
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Old 05-31-2012, 01:54 PM   #2
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Originally Posted by NGSNewbie1 View Post
Sorry for this newbie question but I haven't been able to get an answer after searching around. Is there a program that automagically produces the somatic mutations from inputted tumor and normal VCF files? I'm trying to avoid using a tool like SomaticSniper with BAM files because of size/computation etc. If I have the VCF files, is there an easy way to just select the differences?

Thank you in advance for any guidance!
The thing is that these tools like SomaticSniper are designed to work on the bam files for a reason. Whilst a subtractive approach with VCFs will work for some somatic calls, most genotypers aren't really geared up for variant detection in heterogenous cancer samples.

NGS is not always speedy work, sometimes it's better just to use the tools than take the shortcuts
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Old 05-31-2012, 06:07 PM   #3
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Are there any targeted therapies in the work after you did this type of comparison?
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Old 05-31-2012, 07:46 PM   #4
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An illumina one:

http://www.ncbi.nlm.nih.gov/pubmed/22581179
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Old 05-31-2012, 07:53 PM   #5
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Another one from Canada

http://www.ncbi.nlm.nih.gov/pubmed/22285562
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Old 06-01-2012, 12:40 AM   #6
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Are there any targeted therapies in the work after you did this type of comparison?
If that's directed at me - not in the case of my exome work, but I do work on small, targeted cancer panel development for stratified medicine.

Your also posted Strelka and JointSNVMix - I find the latter somewhat confusing to get to grips with, Strelka is on my to do list. I tend to use VarScan2 for paired comparisons for e.g. copy number. Neither as far as I am concerned answer the question from the OP as they both require BAM files for input.
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Old 06-01-2012, 02:27 PM   #7
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Originally Posted by NGSNewbie1 View Post
Sorry for this newbie question but I haven't been able to get an answer after searching around. Is there a program that automagically produces the somatic mutations from inputted tumor and normal VCF files? I'm trying to avoid using a tool like SomaticSniper with BAM files because of size/computation etc. If I have the VCF files, is there an easy way to just select the differences?

Thank you in advance for any guidance!
While I'm uncertain that the results will really be what you're looking for, this can be done using GATK's SelectVariants with the --discordance flag (see http://www.broadinstitute.org/gsa/ga...tVariants.html for details).

Unfortunately, unless you already have GATK up and running, this is not a trivial task (as getting GATK functioning properly can be a bit tricky).

As mentioned by others though, tumor/normal paired variant calling generally seems to be carried out by a program specifically developed for that purpose (VarScan2, SMUG, and MuTect being the ones with which I am familiar).

Sorry there's not a better answer, but I hope this helps a bit.

Jason
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Old 06-12-2012, 10:10 AM   #8
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Originally Posted by SkinFlayer View Post
While I'm uncertain that the results will really be what you're looking for, this can be done using GATK's SelectVariants with the --discordance flag (see http://www.broadinstitute.org/gsa/ga...tVariants.html for details).

Unfortunately, unless you already have GATK up and running, this is not a trivial task (as getting GATK functioning properly can be a bit tricky).

As mentioned by others though, tumor/normal paired variant calling generally seems to be carried out by a program specifically developed for that purpose (VarScan2, SMUG, and MuTect being the ones with which I am familiar).

Sorry there's not a better answer, but I hope this helps a bit.

Jason
Hi,

Do you know how to annotate the output from MuTect? I have 3800 mutation calls and I am stuck..
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Old 06-14-2012, 04:26 AM   #9
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@shyam_la

I reformatted mine to something that ensembl variant effect predictor can read and went for that during testing.

And to the others - if someone has advice which of the tools out there comes with a good false discovery rate, i am listening.
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Old 06-14-2012, 09:46 PM   #10
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@shyam_la

I reformatted mine to something that ensembl variant effect predictor can read and went for that during testing.

And to the others - if someone has advice which of the tools out there comes with a good false discovery rate, i am listening.
I discovered SNPEff works as well, with MuTect data. Just need removing the redundant columns...
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