Accurity: a tool for inference of tumor purity, tumor cell
ploidy and absolute allelic copy numbers from tumor-normal WGS data
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.
References:
- Zhihui Luo, Xinping Fan, Yao Su and Yu S.Huang
Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants.
Bioinformatics 2018, 34(12), 2004-2011. doi: 10.1093/bioinformatics/bty043
Documentation
Important Notes
- Module Name: Accurity (see the modules page for more information)
- Unusual environment variables set
- ACCURITY_HOME Accurity installation directory
- ACCURITY_BIN Accurity executable directory
- ACCURITY_DATA Accurity sample data directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
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 ~]$exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$