Difference between revisions of "VarDictJava"
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 20:01, 27 May 2022
Description
VarDictJava is a variant discovery program written in Java and Perl. It is a partial Java port of VarDict variant caller.
The original Perl VarDict is a sensitive variant caller for both single and paired sample variant calling from BAM files. VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads and better scalability than Java based variant callers.
Required Modules
Serial
- gcc/5.2.0
- vardictjava
System Variables
- HPC_VARDICTJAVA_DIR - installation directory
- HPC_VARDICTJAVA_BIN - executable directory
Citation
If you publish research that uses vardictjava you have to cite it as follows:
VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research