LumosVar2 is now available!
https://github.com/tgen/lumosVar2/
Designed for calling somatic variants in tumor samples lacking matched normals. Copy number and minor allele copy number are estimated by EM to determine the expected somatic and germline variant allele frequencies at each position. Prior probabilities of germline or somatic variants at each position are calculated based on 1000 genomes allele frequencies or COSMIC counts. A set of unmatched normals is used to find mean read depths and position quality scores.
PREREQUISITES
BAM PREPERATION
Bams should be created using bwa-mem
http://bio-bwa.sourceforge.net/
It is recommended (but not required) to run abra reassembly to improve indel calling and allele frequency estimates
https://github.com/mozack/abra
USAGE
First a set of unmatched controls must be analyzed to find average read depths and position quality metrics:
module load MCR/9.0
./analyzeControls controlsConfig.yaml
When running, the files parsePileupData.packed.pl and indexControlMetrics.sh must be in your working directory specified in the config files. You must also have a text file that lists the paths to the control bams you wish to analyze. You specify the path to your bam list file as well as your samtools and htslib installations, your bed file and your output path in the yaml config file. See configTemplates/controlsConfig.yaml analyzeControls will generate a set of bgzip tabix indexed files (one per chromosome) with quality metrics to be used by the main caller.
To call a tumor bam:
module load MCR/9.0
./callTumorOnly tumorConfig.yaml
When running, the files parsePileupData.packed.pl and cghcbshybridnu.mat must be in the working directory specified in the config files. You specify the path to the bam, as well as the control metrics files, your samtools and htslib installations, your bed file, and your output path in the yaml config file. See configTemplates/tumorConfig.yaml. The caller will produce an SNV and indel VCF (.tumorOnly.all.vcf), a copy number and LOH VCF (.cna.seg.vcf), a clone summary table (.cloneSummary.csv), and a summary figure (.png)