uclahs-cds / pipeline-call-sSNV

A Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
https://uclahs-cds.github.io/pipeline-call-sSNV/
GNU General Public License v2.0
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Add Single-Sample Caller #141

Open pboutros opened 1 year ago

pboutros commented 1 year ago

There's a new, promising method for tumor-only SNV calling: Repository Manuscript

It looks like there are a fair number of downstream tools used/required, so it's not clear how easy this will be.

maotian06 commented 1 year ago

If we want to build it, we can create a new workflow and write processes for each tool, probably ~ 10 processes. Some of the tools, like SnpSift and FPfilter, we have in this or other pipelines; some machine learning tools, we need to build from scratch.

But it would be worth doing so! Our current pipeline's tumor-only model is based on mutect2 and has a lot of false positives. Here is a previous result:

Option Total SNPs %Unique SNPs %Shared SNPs
Paired Normal-Tumor 34,747 14138;40.7% 20,609; 59.3%
Tumor-only 149,053 128,444; 86.2% 20,609; 13.8%

Originally posted by @maotian06 in https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/80