Snakemake pipeline to call SNV in hybridization capture data adapted for multiple samples of a same tumor. (+WIP on CNV calling)
Made following https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2 and https://software.broadinstitute.org/gatk/best-practices/workflow?id=11146
Two conda envs: "root", for bwa and samtools, etc and "plot" for R rules. List of packages found in local
TODO add use-conda in Snakefiles, right now source activate plot is needed only before calling the coverage_plot
rule in align_recalibrate and root is ok for everything else (note that it has more packages than those needed for this project, TODO list).
To produce the GATK singularity image the recipe is in local/src, then
singularity build gatk.img gatk.recipe if you have root access.
Otherwise:
singularity pull --name gatk.img docker://broadinstitute/gatk:4.1.0.0
Right now Snakefiles load the image from ROOT+"/gatk/gatk.img".
singularity pull --name gatk.img docker://etal/cnvkit
Right now Snakefiles load the image from ROOT+"/cnvkit/cnvkit.img".