Accurity infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants. Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage set- tings in which several existing methods perform poorly.
Allocate an interactive session and load the program module:
[user@biowulf]$ sinteractive --mem=48g --cpus-per-task=8 [user@cn3316 ~]$module load AccurityCopy sample data and source code to your current folder:
[user@cn3316 ~]$cp $ACCURITY_DATA/* . [user@cn3316 ~]$cp $ACCURITY_SRC/* .Enter the Accurity singularity container and run the program from within the container:
[user@cn3316 ~]$acc Singularity Accurity.sqsh:>./main.py -c configure -t tumor.bam -n normal.bam -o sample_1_infer -d 1Exit the container and end the interactive session:
Singularity Accurity.sqsh:>exit [user@cn3316 ~]$exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$