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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

• Accurity Home page

• 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

Allocate an interactive session and load the program module:

[user@biowulf]$ sinteractive --mem=48g --cpus-per-task=8
[user@cn3316 ~]$module load Accurity

Copy sample data to your current folder:

[user@cn3316 ~]$cp $ACCURITY_DATA/* .

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 1

Exit the container and end the interactive session:

Singularity Accurity.sqsh:>exit
[user@cn3316 ~]$exit 
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$