Question: Somatic variant caller
0
gravatar for CY
9 weeks ago by
CY10
United States
CY10 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 9 weeks ago by markus.riester70 • written 9 weeks ago by CY10
2
gravatar for markus.riester
9 weeks ago by
markus.riester70 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 9 weeks ago by markus.riester70

Very precise explanation. Thanks

ADD REPLYlink written 9 weeks ago by CY10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1302 users visited in the last hour