Difference between revisions of "Conpair"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DAT - data directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
<!--Configuration--> | <!--Configuration--> | ||
Revision as of 21:02, 6 December 2019
Description
Conpair: concordance and contamination estimator for tumor–normal pairs
Conpair is a fast and robust method dedicated for human tumor-normal studies to perform concordance verification (= samples coming from the same individual), as well as cross-individual contamination level estimation in whole-genome and whole-exome sequencing experiments. Importantly, our method of estimating contamination in the tumor samples is not affected by copy number changes and is able to detect contamination levels as low as 0.1%.
Required Modules
Serial
- gcc/5.2.0
- Conpair
System Variables
- HPC_CONPAIR_DIR - installation directory
- HPC_CONPAIR_BIN - executable directory
- HPC_CONPAIR_DAT - data directory
- HPC_CONPAIR_DOC - documentation directory