> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/chip-variant-calling-and-processing/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/chip-variant-calling-and-processing/clonal-hematopoesis-varaint-calling-and-process.md).

# Clonal Hematopoesis Varaint Calling and Process

Workflow that generates VCF files, which are then annotated and filtered for CMO-CH analysis.

### Introduction <a href="#introduction" id="introduction"></a>

CHIP-VAR pipeline generates VCF and MAF files from the input BAM file which are then processed by the single sample method, annotated by multiple databases and tools, and finally filtered to generate high-confidence Clonal Hematopoetic Putative-Driver (CHPD) calls. Detailed descriptions of the process, tools, and output can be found in this gitbook.&#x20;

### Credits <a href="#credits" id="credits"></a>

* CMO cfDNA Informatics Team<br>