abemus: ABEMUS: Adaptive per Base Error Model in Ultra-deep...
In abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data
Description
The package abemus is a NGS-based computational method that uses control samples to build global and local sequencing error reference models that are then used to improve the detection of somatic SNVs in cfDNA samples.
Details
In step_1 and step_2 only control samples are used to build the per-base error model ( compute_pbem )
and compute both coverage-dependent and coverage-independent allelic fraction thresholds ( compute_afthreshold ).
In step_3 tumor samples are inspected and somatic snvs are called ( callsnvs ) based on both custom filtering criteria (i.e. minimum coverage, minimum number of reads supporting an alternative allele)
and allelic fraction thresholds.
Then in step_4, the per-base error model computed in step 1 is exploited to further refine the final set of putative somatic snvs ( apply_scaling_factor ).
abemus documentation built on Dec. 19, 2019, 1:07 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description
The package abemus is a NGS-based computational method that uses control samples to build global and local sequencing error reference models that are then used to improve the detection of somatic SNVs in cfDNA samples.
Details
In step_1 and step_2 only control samples are used to build the per-base error model ( compute_pbem )
and compute both coverage-dependent and coverage-independent allelic fraction thresholds ( compute_afthreshold ).
In step_3 tumor samples are inspected and somatic snvs are called ( callsnvs ) based on both custom filtering criteria (i.e. minimum coverage, minimum number of reads supporting an alternative allele)
and allelic fraction thresholds.
Then in step_4, the per-base error model computed in step 1 is exploited to further refine the final set of putative somatic snvs ( apply_scaling_factor ).
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.