Question: Somatic variant caller
0
gravatar for CY
5 months ago by
CY30
United States
CY30 wrote:

We are using Illumina's Somatic Variant Caller (https://www.illumina.com/documents/products/technotes/technote_somatic_variant_caller.pdf) to call somatic variant from tumor sample. Based on the Somatic Variant Caller description, it used Poisson model to calculate p-value for each variant to be true. My question is: Does somatic mutation follow poisson distribution? How? Any comments are appreciated. Thanks

ADD COMMENTlink modified 5 months ago by markus.riester180 • written 5 months ago by CY30
3
gravatar for markus.riester
5 months ago by
markus.riester180 wrote:

The variant caller assumes sequencing errors are Poisson distributed. Looks like you get a call when the alt allele has a less than 1% chance of being a sequencing error given the number of supporting reads and the predefined error rate.

ADD COMMENTlink written 5 months ago by markus.riester180

Very precise explanation. Thanks

ADD REPLYlink written 5 months ago by CY30
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