avalind/pajp

Somatic mutation calling on moderately deep WES data using GATK/MuTect

PAJP

Introduction

Snakemake based toolchain for somatic variant calling on tumor/normal pairs of WES data. Implementing GATK best practices for .bam-file processing and then uses MuTect and Scalpel to call SNVs and Indels. Furthermore use contest to estimate cross-sample contamination and generate quality control reports for the bam-files using QualiMap.

The vcf files of called somatic variants are annotated using Annovar.

The config.py script makes some pretty harsh assumptions on how the fastq-files are ordered.

TODO

• Subworkflows.
• uploading of metadata to dropbox etc.