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Finding Somatic Mutations From Whole Exome

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
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updated by Dan Koboldt • Dan Koboldt • written by Angel Angel

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

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written by Rlong • Rlong

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.

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written by Larry_Parnell Larry_Parnell

2 answers

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.

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written by Sean Davis Sean Davis

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

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written by Angel Angel

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

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updated by Ram Ram • written by Dan Koboldt • Dan Koboldt

Thanks very much and I will begin with varscan.

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written by Angel Angel

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