GMS Twist Myeloid pipeline

Poppy

Poppy is a Snakemake pipeline used for analysing hybrid capture short-read sequencing data from the Genomic Medicine Sweden myeloid gene panel. See the publication.

The pipeline analyses tumor-only samples and reports:

• Small variants
• CNVs
• QC report.

It includes a reference pipeline used with normal samples (panel of normals, PoN) to build the necessary files needed to run Poppy.

Gene Panel

The Twist Myeloid gene panel is a short-read capture panel designed for capturing common aberrations in Myeloid disorders which includes a comprehensive gene panel, a CNV backbone, and ID snps. The design is focused on clinical use but can also be used for research applications.