Reference files and a small demo file for MisMatchFinder

This Zenodo repository contains the reference files and a small demo file for running MisMatchFinder. MisMatchFinder is a fast computational tool for detecting variants and infering mutational signatures from plasma low-coverage, next generation sequencing data of cancer patients without using sequencing from matched normal tissues. MisMatchFinder is developed by the Molecular Biomarkers and Translational Genomics Lab in Peter MacCallum Cancer Centre (Australia). The tool and instructions are available at the following Bitbucket repository. To run the tool, it is highly recommanded to activate the germline filter to filter out common germline variants and use a whitelist which helps to only detect variants in high mappability regions of the human genome. For example: $ mismatchfinder --germline_file /path/to/echtvarfile/gnomad.v3.1.2.echtvar.v2.zip --whitelist_bed /path/to/whitelist.bed -o /path/to/outputfolder/ --strict_overlaps --only_overlaps /path/to/plasma_DNA_demo.bam The files included in this dataset are described below: gnomad.v3.1.2.echtvar.v2.zip: the pre-built gnomad data used for the MisMatchFinder germline filter. GCA_000001405.15_GRCh38_full_analysis_set.100mer.highMappability.bed: the high mappability regions file for the GRCh38 human genome, used as the MisMatchFinder whitelist. Note, the plasma_DNA_demo.bam is simulated human plasma sequencing data of chromosome 19. This file and the corresponding MisMatchFinder output (plasma_DNA_demo_bamsites.vcf.gz) should only be used for the sanity testing of MisMatchFinder.