This repository contains source code behind this preprint:
https://www.medrxiv.org/content/10.1101/2020.05.26.20089888v1
- Initial processing of the whole-genome sequencing data, including SNP and CNV calling, was performed with the DKFZ/PCAWG WGS analysis workflow, available as a Docker container from:
https://dockstore.org/containers/quay.io/pancancer/pcawg-dkfz-workflow
Structural variant identification with SOPHIA:
https://bitbucket.org/utoprak/sophia/src
- A compatible CWL worfklow for the intial processing ot the whole-genome bisulfite data, from reads to methylation calls:
https://github.com/CompEpigen/WGBS_workflows/CWL/workflows/BWA_meth_start_with_trimmed.cwl
- A compatible CWL workflow for ATAC-seq data, from reads to genome signal tracks, is available from:
https://github.com/CompEpigen/ATACseq_workflows
- A compatible CWL workflow for ChIPmentation data, from reads to genome signal tracks:
https://github.com/CompEpigen/ChIPseq_workflows
- A snakemake-based processing workflow for RNA-seq data:
https://github.com/CompEpigen/RNASeq_GCTB.
- Code for calling of LMDs from WGBS data: