ITHE implements a somatic variant post-processing pipeline using a system of Perl and Bash scripts. ITHE can be used to call SNV variants and estimate the intratumor heterogeneity between two samples per individual, given a set of user-specified parameters. ITHE can also be used to optimize the parameters that regulate its execution empirically, using technical replicates (same DNA sample sequenced twice independently). ITHE is intended to be run on an HPC environment, interacting directly with a workload manager supporting dependencies between jobs. We developed ITHE on a SLURM environment, but its flexible configuration should make it easy to run it under other workload managers of similar characteristics.
IntraTumor Heterogeneity Estimator (ITHE).
FORTUNATO A.
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2021-01-01
Abstract
ITHE implements a somatic variant post-processing pipeline using a system of Perl and Bash scripts. ITHE can be used to call SNV variants and estimate the intratumor heterogeneity between two samples per individual, given a set of user-specified parameters. ITHE can also be used to optimize the parameters that regulate its execution empirically, using technical replicates (same DNA sample sequenced twice independently). ITHE is intended to be run on an HPC environment, interacting directly with a workload manager supporting dependencies between jobs. We developed ITHE on a SLURM environment, but its flexible configuration should make it easy to run it under other workload managers of similar characteristics.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
