Question: inconsistency between somatic SNV from Varscan and SNV from Samtools
1
gravatar for dingxm
3.9 years ago by
dingxm20
United States
dingxm20 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.

Best

snp • 1.2k views
ADD COMMENTlink modified 3.9 years ago by Sean Davis25k • written 3.9 years ago by dingxm20
0
gravatar for Sean Davis
3.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k 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 COMMENTlink written 3.9 years ago by Sean Davis25k
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 REPLYlink written 3.9 years ago by dingxm20

Yes.  

ADD REPLYlink written 3.9 years ago by Sean Davis25k
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