Question: Finding Somatic Mutations From Whole Exome
1
gravatar for Angel
7.9 years ago by
Angel210
United States
Angel210 wrote:

Q1) How do I call and report somatic mutations after getting the vcf files as below?

samtools mpileup -u hg19.fa foo.sorted.bam | bcftools view - > foo.sorted.bcf

bcftools view food.sorted.bcf | vcfutils varFilter -D200 > foo.d200.flt.vcf
exome mutation • 3.1k views
ADD COMMENTlink modified 7.8 years ago by Dan Koboldt60 • written 7.9 years ago by Angel210

Do you have a matched normal sample? Without a comparison, you won't be able to tell somatic from germline mutations.

ADD REPLYlink written 7.8 years ago by Rlong340

It is not likely that all cells whose DNA was sequenced originated from the same clonal population. It is much more likely, especially for a clinical sample, that they've sequenced a mixture of cells of different origins, and hence different genomes. A matched normal is helpful, but may not be necessary.

ADD REPLYlink written 7.8 years ago by Larry_Parnell16k
4
gravatar for Sean Davis
7.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Take a look at the -T pair option of bcftools. A non-comprehensive list of somatic variant callers includes varscan, somatic sniper, joint-snv-mix, and mutect (licensed from the broad). I suspect that many folks use a custom script for this application, though.

ADD COMMENTlink written 7.9 years ago by Sean Davis25k

Thanks so much. Sorry again for my delayed response. I will be trying some of these today.

ADD REPLYlink written 7.8 years ago by Angel210
3
gravatar for Dan Koboldt
7.8 years ago by
Dan Koboldt60
Dan Koboldt60 wrote:

For exome sequencing of tumor-normal pairs, we use VarScan and SomaticSniper.

ADD COMMENTlink modified 8 weeks ago by RamRS24k • written 7.8 years ago by Dan Koboldt60

Thanks very much and I will begin with varscan.

ADD REPLYlink written 7.8 years ago by Angel210

VarScan2 is out:

http://genome.cshlp.org/cgi/content/abstract/gr.129684.111v1

ADD REPLYlink written 7.8 years ago by Sean Davis25k
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