Question: Somatic variant caller
0
gravatar for CY
2.2 years ago by
CY330
United States
CY330 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 Biostar ♦♦ 20 • written 2.2 years ago by CY330
3
gravatar for markus.riester
2.2 years ago by
markus.riester400 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 2.2 years ago by markus.riester400

Very precise explanation. Thanks

ADD REPLYlink written 2.2 years ago by CY330
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