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Question: inconsistency between somatic SNV from Varscan and SNV from Samtools
1
gravatar for dingxm
5.7 years ago by
dingxm • 20
United States
dingxm • 20 wrote:

HI all

I have two paired samples. One is Normal and the other is Tumor. I called SNP of both samples using Samtools/bcftools  and then call somatic mutation using Varscan2. I get some somatic mutation from Varscan. But these mutation are not among the mutation list of tumor sample I got from samtools. Can someone help to explain.

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snp • 1.6k views
ADD COMMENT • link •
modified 5.7 years ago by Sean Davis ♦ 26k • written 5.7 years ago by dingxm • 20
0
gravatar for Sean Davis
5.7 years ago by
Sean Davis ♦ 26k
National Institutes of Health, Bethesda, MD
Sean Davis ♦ 26k wrote:

The two variant callers use very different theory for calling variants, so it is not surprising that the two give different results.  It turns out that VarScan is very sensitive (or noisy, depending on your point-of-view) while samtools is less noisy.  In practice, VarScan often needs to be further filtered to get reliable variants.
ADD COMMENT • link written 5.7 years ago by Sean Davis ♦ 26k
1

Sean Thanks for your reply. These somatic mutations were got after strict filter. Is that possible these somatic mutations have low allele frequency and was not called as germline SNP by Samtools?

ADD REPLY • link written 5.7 years ago by dingxm • 20

Yes.  

ADD REPLY • link written 5.7 years ago by Sean Davis ♦ 26k
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